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https://www.readbyqxmd.com/read/27422445/pm55-a-developmental-stage-and-tissue-specific-powdery-mildew-resistance-gene-introgressed-from-dasypyrum-villosum-into-common-wheat
#1
Ruiqi Zhang, Bingxiao Sun, Juan Chen, Aizhong Cao, Liping Xing, Yigao Feng, Caixia Lan, Peidu Chen
Powdery mildew resistance gene Pm55 was physically mapped to chromosome arm 5VS FL 0.60-0.80 of Dasypyrum villosum . Pm55 is present in T5VS·5AL and T5VS·5DL translocations, which should be valuable resources for wheat improvement. Powdery mildew caused by Blumeria graminis f. sp. tritici is a major wheat disease worldwide. Exploiting novel genes effective against powdery mildew from wild relatives of wheat is a promising strategy for controlling this disease. To identify novel resistance genes for powdery mildew from Dasypyrum villosum, a wild wheat relative, we evaluated a set of Chinese Spring-D...
October 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27280472/mutations-affecting-potassium-import-restore-the-viability-of-the-escherichia-coli-dna-polymerase-iii-hold-mutant
#2
Adeline Durand, Anurag Kumar Sinha, Cloelia Dard-Dascot, Bénédicte Michel
Mutants lacking the ψ (HolD) subunit of the Escherichia coli DNA Polymerase III holoenzyme (Pol III HE) have poor viability, but a residual growth allows the isolation of spontaneous suppressor mutations that restore ΔholD mutant viability. Here we describe the isolation and characterization of two suppressor mutations in the trkA and trkE genes, involved in the main E. coli potassium import system. Viability of ΔholD trk mutants is abolished on media with low or high K+ concentrations, where alternative K+ import systems are activated, and is restored on low K+ concentrations by the inactivation of the alternative Kdp system...
June 2016: PLoS Genetics
https://www.readbyqxmd.com/read/26804569/structures-of-the-dfsb-protein-family-suggest-a-cationic-helical-sibling-lethal-factor-peptide
#3
Jonathan D Taylor, Gabrielle Taylor, Stephen A Hare, Steve J Matthews
Bacteria have developed a variety of mechanisms for surviving harsh environmental conditions, nutrient stress and overpopulation. Paenibacillus dendritiformis produces a lethal protein (Slf) that is able to induce cell death in neighbouring colonies and a phenotypic switch in more distant ones. Slf is derived from the secreted precursor protein, DfsB, after proteolytic processing. Here, we present new crystal structures of DfsB homologues from a variety of bacterial species and a surprising version present in the yeast Saccharomyces cerevisiae...
February 13, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/26527643/a-dinb-ortholog-enables-mycobacterial-growth-under-dttp-limiting-conditions-induced-by-the-expression-of-a-mycobacteriophage-derived-ribonucleotide-reductase-gene
#4
Shreya Ghosh, Sourabh Samaddar, Prithwiraj Kirtania, Sujoy K Das Gupta
UNLABELLED: Mycobacterium species such as M. smegmatis and M. tuberculosis encode at least two translesion synthesis (TLS) polymerases, DinB1 and DinB2, respectively. Although predicted to be linked to DNA repair, their role in vivo remains enigmatic. M. smegmatis mc(2)155, a strain commonly used to investigate mycobacterial genetics, has two copies of dinB2, the gene that codes for DinB2, by virtue of a 56-kb chromosomal duplication. Expression of a mycobacteriophage D29 gene (gene 50) encoding a class II ribonucleotide reductase in M...
January 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/26352807/a-genetic-selection-for-dinb-mutants-reveals-an-interaction-between-dna-polymerase-iv-and-the-replicative-polymerase-that-is-required-for-translesion-synthesis
#5
Michelle K Scotland, Justin M H Heltzel, James E Kath, Jung-Suk Choi, Anthony J Berdis, Joseph J Loparo, Mark D Sutton
Translesion DNA synthesis (TLS) by specialized DNA polymerases (Pols) is a conserved mechanism for tolerating replication blocking DNA lesions. The actions of TLS Pols are managed in part by ring-shaped sliding clamp proteins. In addition to catalyzing TLS, altered expression of TLS Pols impedes cellular growth. The goal of this study was to define the relationship between the physiological function of Escherichia coli Pol IV in TLS and its ability to impede growth when overproduced. To this end, 13 novel Pol IV mutants were identified that failed to impede growth...
September 2015: PLoS Genetics
https://www.readbyqxmd.com/read/26218456/point-mutations-in-escherichia-coli-dna-pol-v-that-confer-resistance-to-non-cognate-dna-damage-also-alter-protein-protein-interactions
#6
Lisa A Hawver, Mohammad Tehrani, Nicole M Antczak, Danielle Kania, Stephanie Muser, Jana Sefcikova, Penny J Beuning
Y-family DNA polymerases are important for conferring cellular resistance to DNA damaging agents in part due to their specialized ability to copy damaged DNA. The Escherichia coli Y-family DNA polymerases are encoded by the umuDC and dinB genes. UmuC and the cleaved form of UmuD, UmuD', form UmuD'2C (pol V), which is able to bypass UV photoproducts such as cyclobutane pyrimidine dimers and 6-4 thymine-thymine dimers, whereas DinB is specialized to copy N(2)-dG adducts, such as N(2)-furfuryl-dG. To better understand this inherent specificity, we used hydroxylamine to generate a random library of UmuC variants from which we then selected those with the ability to confer survival to nitrofurazone (NFZ), which is believed to cause N(2)-furfuryl-dG lesions...
October 2015: Mutation Research
https://www.readbyqxmd.com/read/26154586/-1-h-13-c-and-15-n-backbone-resonance-assignments-of-the-full-length-40%C3%A2-kda-s-acidocaldarius-y-family-dna-polymerase-dinb-homolog
#7
Sean L Moro, Melanie J Cocco
The dinB homolog (Dbh) is a member of the Y-family of translesion DNA polymerases, which are specialized to accurately replicate DNA across from a wide variety of lesions in living cells. Lesioned bases block the progression of high-fidelity polymerases and cause detrimental replication fork stalling; Y-family polymerases can bypass these lesions. The active site of the translesion synthesis polymerase is more open than that of a replicative polymerase; consequently Dbh polymerizes with low fidelity. Bypass polymerases also have low processivity...
October 2015: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/26147350/the-protein-level-of-rev1-a-tls-polymerase-in-fission-yeast-is-strictly-regulated-during-the-cell-cycle-and-after-dna-damage
#8
Masashi Uchiyama, Junko Terunuma, Fumio Hanaoka
Translesion DNA synthesis provides an alternative DNA replication mechanism when template DNA is damaged. In fission yeast, Eso1 (polη), Kpa1/DinB (polκ), Rev1, and Polζ (a complex of Rev3 and Rev7) have been identified as translesion synthesis polymerases. The enzymatic characteristics and protein-protein interactions of these polymerases have been intensively characterized; however, how these proteins are regulated during the cell cycle remains unclear. Therefore, we examined the cell cycle oscillation of translesion polymerases...
2015: PloS One
https://www.readbyqxmd.com/read/26136829/development-of-a-stress-induced-mutagenesis-module-for-autonomous-adaptive-evolution-of-escherichia-coli-to-improve-its-stress-tolerance
#9
Linjiang Zhu, Yin Li, Zhen Cai
BACKGROUND: Microbial tolerance to different environmental stresses is of importance for efficient production of biofuels and biochemical. Such traits are often improved by evolutionary engineering approaches including mutagen-induced mutagenesis and successive passage. In contrast to these approaches which generate mutations in rapidly growing cells, recent research showed that mutations could be generated in non-dividing cells under stressful but non-lethal conditions, leading to the birth of the theory of stress-induced mutagenesis (SIM)...
2015: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/26134316/the-origin-of-mutants-under-selection-how-natural-selection-mimics-mutagenesis-adaptive-mutation
#10
REVIEW
Sophie Maisnier-Patin, John R Roth
Selection detects mutants but does not cause mutations. Contrary to this dictum, Cairns and Foster plated a leaky lac mutant of Escherichia coli on lactose medium and saw revertant (Lac(+)) colonies accumulate with time above a nongrowing lawn. This result suggested that bacteria might mutagenize their own genome when growth is blocked. However, this conclusion is suspect in the light of recent evidence that revertant colonies are initiated by preexisting cells with multiple copies the conjugative F'lac plasmid, which carries the lac mutation...
July 2015: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/26100038/interactions-and-localization-of-escherichia-coli-error-prone-dna-polymerase-iv-after-dna-damage
#11
Sarita Mallik, Ellen M Popodi, Andrew J Hanson, Patricia L Foster
UNLABELLED: Escherichia coli's DNA polymerase IV (Pol IV/DinB), a member of the Y family of error-prone polymerases, is induced during the SOS response to DNA damage and is responsible for translesion bypass and adaptive (stress-induced) mutation. In this study, the localization of Pol IV after DNA damage was followed using fluorescent fusions. After exposure of E. coli to DNA-damaging agents, fluorescently tagged Pol IV localized to the nucleoid as foci. Stepwise photobleaching indicated ∼60% of the foci consisted of three Pol IV molecules, while ∼40% consisted of six Pol IV molecules...
September 2015: Journal of Bacteriology
https://www.readbyqxmd.com/read/25837992/next-generation-sequencing-reveals-the-biological-significance-of-the-n-2-3-ethenoguanine-lesion-in-vivo
#12
Shiou-chi Chang, Bogdan I Fedeles, Jie Wu, James C Delaney, Deyu Li, Linlin Zhao, Plamen P Christov, Emily Yau, Vipender Singh, Marco Jost, Catherine L Drennan, Lawrence J Marnett, Carmelo J Rizzo, Stuart S Levine, F Peter Guengerich, John M Essigmann
Etheno DNA adducts are a prevalent type of DNA damage caused by vinyl chloride (VC) exposure and oxidative stress. Etheno adducts are mutagenic and may contribute to the initiation of several pathologies; thus, elucidating the pathways by which they induce cellular transformation is critical. Although N(2),3-ethenoguanine (N(2),3-εG) is the most abundant etheno adduct, its biological consequences have not been well characterized in cells due to its labile glycosidic bond. Here, a stabilized 2'-fluoro-2'-deoxyribose analog of N(2),3-εG was used to quantify directly its genotoxicity and mutagenicity...
June 23, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25706748/expression-and-mutational-analysis-of-dinb-like-protein-dr0053-in-deinococcus-radiodurans
#13
Deepti Appukuttan, Ho Seong Seo, Sunwook Jeong, Sunghun Im, Minho Joe, Dusup Song, Jungjoon Choi, Sangyong Lim
In order to understand the mechanism governing radiation resistance in Deinococcus radiodurans, current efforts are aimed at identifying potential candidates from a large repertoire of unique Deinococcal genes and protein families. DR0053 belongs to the DinB/YfiT protein family, which is an over-represented protein family in D. radiodurans. We observed that dr0053 transcript levels were highly induced in response to gamma radiation (γ-radiation) and mitomycin C (MMC) exposure depending on PprI, RecA and the DrtR/S two-component signal transduction system...
2015: PloS One
https://www.readbyqxmd.com/read/25684709/steric-gate-residues-of-y-family-dna-polymerases-dinb-and-pol-kappa-are-crucial-for-dntp-induced-conformational-change
#14
Philip Nevin, John R Engen, Penny J Beuning
Discrimination against ribonucleotides by DNA polymerases is critical to preserve DNA integrity. For many DNA polymerases, including those of the Y family, rNTP discrimination has been attributed to steric clashes between a residue near the active site, the steric gate, and the 2'-hydroxyl of the incoming rNTP. Here we used hydrogen/deuterium exchange (HDX) mass spectrometry (MS) to probe the effects of the steric gate in the Y-family DNA polymerases Escherichia coli DinB and human DNA pol κ. Formation of a ternary complex with a G:dCTP base pair in the active site resulted in slower hydrogen exchange relative to a ternary complex with G:rCTP in the active site...
May 2015: DNA Repair
https://www.readbyqxmd.com/read/25628359/recombinase-and-translesion-dna-polymerase-decrease-the-speed-of-replication-fork-progression-during-the-dna-damage-response-in-escherichia-coli-cells
#15
Kang Wei Tan, Tuan Minh Pham, Asako Furukohri, Hisaji Maki, Masahiro Tatsumi Akiyama
The SOS response is a DNA damage response pathway that serves as a general safeguard of genome integrity in bacteria. Extensive studies of the SOS response in Escherichia coli have contributed to establishing the key concepts of cellular responses to DNA damage. However, how the SOS response impacts on the dynamics of DNA replication fork movement remains unknown. We found that inducing the SOS response decreases the mean speed of individual replication forks by 30-50% in E. coli cells, leading to a 20-30% reduction in overall DNA synthesis...
February 18, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25200080/characterization-of-three-mycobacterial-dinb-dna-polymerase-iv-paralogs-highlights-dinb2-as-naturally-adept-at-ribonucleotide-incorporation
#16
Heather Ordonez, Maria Loressa Uson, Stewart Shuman
This study unveils Mycobacterium smegmatis DinB2 as the founder of a clade of Y-family DNA polymerase that is naturally adept at incorporating ribonucleotides by virtue of a leucine in lieu of a canonical aromatic steric gate. DinB2 efficiently scavenges limiting dNTP and rNTP substrates in the presence of manganese. DinB2's sugar selectivity factor, gauged by rates of manganese-dependent dNMP versus rNMP addition, is 2.7- to 3.8-fold. DinB2 embeds ribonucleotides during DNA synthesis when rCTP and dCTP are at equimolar concentration...
2014: Nucleic Acids Research
https://www.readbyqxmd.com/read/24957605/dna-polymerase-iv-mediates-efficient-and-quick-recovery-of-replication-forks-stalled-at-n2-dg-adducts
#17
Mio Ikeda, Asako Furukohri, Gaelle Philippin, Edward Loechler, Masahiro Tatsumi Akiyama, Tsutomu Katayama, Robert P Fuchs, Hisaji Maki
Escherichia coli DNA polymerase IV (Pol IV, also known as DinB) is a Y-family DNA polymerase capable of catalyzing translesion DNA synthesis (TLS) on certain DNA lesions, and accumulating data suggest that Pol IV may play an important role in copying various kinds of spontaneous DNA damage including N(2)-dG adducts and alkylated bases. Pol IV has a unique ability to coexist with Pol III on the same β clamp and to positively dissociate Pol III from β clamp in a concentration-dependent manner. Reconstituting the entire process of TLS in vitro using E...
July 2014: Nucleic Acids Research
https://www.readbyqxmd.com/read/24914188/selection-of-dinb-alleles-suppressing-survival-loss-upon-dinb-overexpression-in-escherichia-coli
#18
Ryan W Benson, Tiziana M Cafarelli, Thomas J Rands, Ida Lin, Veronica G Godoy
Escherichia coli strains overproducing DinB undergo survival loss; however, the mechanisms regulating this phenotype are poorly understood. Here we report a genetic selection revealing DinB residues essential to effect this loss-of-survival phenotype. The selection uses strains carrying both an antimutator allele of DNA polymerase III (Pol III) α-subunit (dnaE915) and either chromosomal or plasmid-borne dinB alleles. We hypothesized that dnaE915 cells would respond to DinB overproduction differently from dnaE(+) cells because the dnaE915 allele is known to have an altered genetic interaction with dinB(+) compared to its interaction with dnaE(+)...
August 15, 2014: Journal of Bacteriology
https://www.readbyqxmd.com/read/24821014/purification-and-characterization-of-the-staphylococcus-aureus-bacillithiol-transferase-bsta
#19
Varahenage R Perera, Gerald L Newton, Jonathan M Parnell, Elizabeth A Komives, Kit Pogliano
BACKGROUND: Gram-positive bacteria in the phylum Firmicutes synthesize the low molecular weight thiol bacillithiol rather than glutathione or mycothiol. The bacillithiol transferase YfiT from Bacillus subtilis was identified as a new member of the recently discovered DinB/YfiT-like Superfamily. Based on structural similarity using the Superfamily program, we have determined 30 of 31 Staphylococcus aureus strains encode a single bacillithiol transferase from the DinB/YfiT-like Superfamily, while the remaining strain encodes two proteins...
September 2014: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/24763694/cationic-antimicrobial-peptides-promote-microbial-mutagenesis-and-pathoadaptation-in-chronic-infections
#20
RANDOMIZED CONTROLLED TRIAL
Dominique H Limoli, Andrea B Rockel, Kurtis M Host, Anuvrat Jha, Benjamin T Kopp, Thomas Hollis, Daniel J Wozniak
Acquisition of adaptive mutations is essential for microbial persistence during chronic infections. This is particularly evident during chronic Pseudomonas aeruginosa lung infections in cystic fibrosis (CF) patients. Thus far, mutagenesis has been attributed to the generation of reactive species by polymorphonucleocytes (PMN) and antibiotic treatment. However, our current studies of mutagenesis leading to P. aeruginosa mucoid conversion have revealed a potential new mutagen. Our findings confirmed the current view that reactive oxygen species can promote mucoidy in vitro, but revealed PMNs are proficient at inducing mucoid conversion in the absence of an oxidative burst...
April 2014: PLoS Pathogens
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