Mechanisms of DNA damage, repair, and mutagenesis by Chatterjee, Nimrat, Walker, Graham C.

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New CRISPR Mutagenesis Strategies Reveal Variation in Repair Mechanisms among Fungi by Vyas, Valmik K., Bushkin, G. Guy, Bernstein, Douglas A., Sewastianik, Magdalena, Barrasa, M. Inmaculada, Getz, Matthew Aaron, Bartel, David, Fink, Gerald R

“…We have created new vectors for clustered regularly interspaced short palindromic repeat (CRISPR) mutagenesis in Candida albicans, Saccharomyces cerevisiae, Candida glabrata, and Naumovozyma castellii These new vectors permit a comparison of the requirements for CRISPR mutagenesis in each of these species and reveal different dependencies for repair of the Cas9 double-stranded break. …”
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A mutagenesis screen for essential plastid biogenesis genes in human malaria parasites by Hari, Sanjay B., Sauer, Rober T.

“…To discover organellar pathways with evolutionary and biomedical significance, we performed a mutagenesis screen for essential genes required for apicoplast biogenesis in Plasmodium falciparum. …”
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The transcription elongation factor NusA is required for stressinduced mutagenesis in Escherichia coli by Cohen, Susan E., Walker, Graham C.

“…Stress-induced mutagenesis describes the accumulation of mutations that occur in nongrowing cells, in contrast to mutagenesis that occurs in actively dividing populations, and has been referred to as stationary-phase or adaptive mutagenesis. …”
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Position specific variation in the rate of evolution in transcription factor binding sites by Kellis, Manolis, Moses, Alan M., Chiang, Derek Y., Eisen, Michael B., Lander, Eric Steven

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A stapled POL κ peptide targets REV1 to inhibit mutagenic translesion synthesis by Chatterjee, Nimrat, D'Souza, Sanjay, Shabab, Mohammad, Harris, Cynthia A, Hilinski, Gerard J, Verdine, Gregory L, Walker, Graham C

“…The tightest-binding stapled peptide translocates into cells and enhances the cytotoxicity of DNA damaging agents while reducing mutagenesis. Drugs with these characteristics could potentially serve as adjuvants to improve chemotherapy and reduce acquired resistance by inhibiting Rev1-dependent mutagenic translesion synthesis.…”
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Y-family DNA polymerases in Escherichia coli by Jarosz, Daniel F., Beuning, Penny J., Cohen, Susan E., Walker, Graham C.

“…The observation that mutations in the Escherichia coli genes umuC+ and umuD+ abolish mutagenesis induced by UV light strongly supported the counterintuitive notion that such mutagenesis is an active rather than passive process. …”
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A Strategic Approach for Fluorescence Imaging of Membrane Proteins in a Native-like Environment by Swiecicki, Jean-Marie, Santana, Jordan Tyler, Imperiali, Barbara

“…Herein, we focus on complementing current methods by integrating the powerful processes of unnatural amino acid mutagenesis, bioorthogonal labeling, and the detergent-free membrane protein solubilization based on the amphiphilic styrene-maleic acid (SMA) polymer. …”
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Redox-dependent rearrangements of the NiFeS cluster of carbon monoxide dehydrogenase by Wittenborn, Elizabeth Charlot, Drennan, Catherine L

“…Combined with supporting spectroscopic data, our structures reveal that this novel, oxidized cluster arrangement plays a role in avoiding irreversible oxidative degradation at the C-cluster. Furthermore, mutagenesis of a conserved cysteine residue that binds the C-cluster in the oxidized state but not in the reduced state suggests that the oxidized conformation could be important for proper cluster assembly, in particular Ni incorporation. …”
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Identification, characterization and benefits of an exclusion system in an integrative and conjugative element of Bacillus subtilis by Avello, Monika, Davis, Kathleen P, Grossman, Alan Davis

“…This inhibition (exclusion) was specific to the cognate conjugation machinery and the ICEBs1 gene yddJ was both necessary and sufficient to mediate exclusion by recipient cells. Through a mutagenesis and enrichment screen, we identified exclusion-resistant mutations in the ICEBs1 gene conG. …”
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Characterizing the portability of phage-encoded homologous recombination proteins by Filsinger, Gabriel T, Wannier, Timothy M, Pedersen, Felix B, Lutz, Isaac D, Zhang, Julie, Stork, Devon A, Debnath, Anik, Gozzi, Kevin, Kuchwara, Helene, Volf, Verena, Wang, Stan, Rios, Xavier, Gregg, Christopher J, Lajoie, Marc J, Shipman, Seth L, Aach, John, Laub, Michael T, Church, George M

“…Finally, we find that high-efficiency HR far surpasses the mutational capacity of commonly used random mutagenesis methods, generating exceptional phenotypes that are inaccessible through sequential nucleotide conversions. …”
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Global gene disruption in human cells to assign genes to phenotypes by Ploegh, Hidde, Yuan, Bingbing B., Carette, Jan E., Guimaraes, Carla P., Wuethrich, Irene, Blomen, Vincent A., Varadarajan, Malini, Sun, Chong, Bell, George W., Muellner, Markus K., Nijman, Sebastian M., Brummelkamp, Thijn R.

“…Insertional mutagenesis in a haploid background can disrupt gene function[superscript 1]. …”
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Unconventional Ubiquitin Recognition by the Ubiquitin-Binding Motif within the Y-Family DNA Polymerases ι and Rev1 by D'Souza, Sanjay Victor, Walker, Graham C., Bomar, Martha G., Bienko, Marzena, Dikic, Ivan, Zhou, Pei

“…In contrast, only the second UBM of Saccharomyces cerevisiae Rev1 binds to ubiquitin and is essential for Rev1-dependent cell survival and mutagenesis. Point mutations disrupting the UBM-ubiquitin interaction also impair the accumulation of pol ι in replication foci and Rev1-mediated DNA damage tolerance in vivo.…”
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The structural basis of RNA-catalyzed RNA polymerization by Shechner, David M, Bartel, David, Shechner, David M.

“…Two phosphates and the nucleophile jointly coordinate an active-site metal ion. Atomic mutagenesis experiments demonstrate that active-site nucleobase and hydroxyl groups also participate directly in catalysis, collectively playing a role that in proteinaceous polymerases is performed by a second metal ion. …”
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Structural Basis of an N-Degron Adaptor with More Stringent Specificity by Stein, Benjamin Joseph, Grant, Robert A., Sauer, Robert T., Baker, Tania

“…The basis of this enhanced specificity is addressed by crystal structures of ClpS2, with and without ligand, and structure-guided mutagenesis, revealing protein conformational changes and remodeling in the substrate-binding pocket. …”
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JDP2: An oncogenic bZIP transcription factor in T cell acute lymphoblastic leukemia by Mansour, Marc R., He, Shuning, Li, Zhaodong, Lobbardi, Riadh, Abraham, Brian J., Hug, Clemens, Rahman, Sunniyat, Leon, Theresa E., Kuang, You-Yi, Zimmerman, Mark W., Blonquist, Traci, Gjini, Evisa, Gutierrez, Alejandro, Tang, Qin, Garcia-Perez, Laura, Pike-Overzet, Karin, Anders, Lars, Berezovskaya, Alla, Zhou, Yi, Zon, Leonard I., Neuberg, Donna, Fielding, Adele K., Staal, Frank J.T., Langenau, David M., Sanda, Takaomi, Look, A. Thomas, Young, Richard A.

“…JDP2 encodes a bZIP protein that has been implicated as a T-ALL oncogene from insertional mutagenesis studies in mice, but its role in human T-ALL pathogenesis has remained obscure. …”
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Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants by Liou, Geoffrey, Chiang, Ying-Chih, Wang, Yi, Weng, Jing-Ke

“…In vivo complementation, in vitro biochemical and mutagenesis analyses, and molecular dynamics simulations identified a set of residues that differ between basal-plant and euphyllophyte CHSs and modulate catalytic cysteine reactivity. …”
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Multi-pathway DNA-repair reporters reveal competition between end-joining, single-strand annealing and homologous recombination at Cas9-induced DNA double-strand breaks by van de Kooij, Bert, Kruswick, Alex, van Attikum, Haico, Yaffe, Michael B

“…<jats:title>Abstract</jats:title><jats:p>DNA double-strand breaks (DSB) are repaired by multiple distinct pathways, with outcomes ranging from error-free repair to mutagenesis and genomic loss. DSB-repair pathway cross-talk and compensation is incompletely understood, despite its importance for genomic stability, oncogenesis, and genome editing using CRISPR/Cas9. …”
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Variants of the elongator protein 3 (ELP3) gene are associated with motor neuron degeneration by Horvitz, Howard Robert

“…In the second, an independent mutagenesis screen in Drosophila for genes important in neuronal communication and survival identified two different loss of function mutations, both in ELP3 (R475K and R456K). …”
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Nucleotide Binding and Conformational Switching in the Hexameric Ring of a AAA+ Machine by Stinson, Benjamin Michael, Nager, Andrew Ross, Glynn, Steven E., Schmitz, Karl R., Baker, Tania, Sauer, Robert T

“…In multiple crystal structures, some ClpX subunits adopt nucleotide-loadable conformations, others adopt unloadable conformations, and each conformational class exhibits substantial variability. Using mutagenesis of individual subunits in covalently tethered hexamers together with fluorescence methods to assay the conformations and nucleotide-binding properties of these subunits, we demonstrate that dynamic interconversion between loadable and unloadable conformations is required to couple ATP hydrolysis by ClpX to mechanical work. …”
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