scholarly journals Promutagenicity of 8-Chloroguanine, A Major Inflammation-Induced Halogenated DNA Lesion

Molecules ◽  
2019 ◽  
Vol 24 (19) ◽  
pp. 3507 ◽  
Author(s):  
Yi Kou ◽  
Myong-Chul Koag ◽  
Seongmin Lee
Keyword(s):  
Hypochlorous Acid ◽  
Kinetic Studies ◽  
Structural Basis ◽  
Base Pairs ◽  
Dna Lesion ◽  
Nucleotide Incorporation ◽  
Reactive Halogen Species ◽  
Induced Mutagenesis ◽  
Hoogsteen Base Pairing ◽  
Halogen Species

Chronic inflammation is closely associated with cancer development. One possible mechanism for inflammation-induced carcinogenesis is DNA damage caused by reactive halogen species, such as hypochlorous acid, which is released by myeloperoxidase to kill pathogens. Hypochlorous acid can attack genomic DNA to produce 8-chloro-2′-deoxyguanosine (ClG) as a major lesion. It has been postulated that ClG promotes mutagenic replication using its syn conformer; yet, the structural basis for ClG-induced mutagenesis is unknown. We obtained crystal structures and kinetics data for nucleotide incorporation past a templating ClG using human DNA polymerase β (polβ) as a model enzyme for high-fidelity DNA polymerases. The structures showed that ClG formed base pairs with incoming dCTP and dGTP using its anti and syn conformers, respectively. Kinetic studies showed that polβ incorporated dGTP only 15-fold less efficiently than dCTP, suggesting that replication across ClG is promutagenic. Two hydrogen bonds between syn-ClG and anti-dGTP and a water-mediated hydrogen bond appeared to facilitate mutagenic replication opposite the major halogenated guanine lesion. These results suggest that ClG in DNA promotes G to C transversion mutations by forming Hoogsteen base pairing between syn-ClG and anti-G during DNA synthesis.

scholarly journals Reading and Misreading 8-oxoguanine, a Paradigmatic Ambiguous Nucleobase

Crystals ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 269 ◽  
Author(s):  
Anna V. Yudkina ◽  
Evgeniy S. Shilkin ◽  
Anton V. Endutkin ◽  
Alena V. Makarova ◽  
Dmitry O. Zharkov
Keyword(s):  
Dna Polymerases ◽  
Structural Basis ◽  
Protective Mechanism ◽  
Dna Glycosylases ◽  
Base Pairs ◽  
Mutagenic Potential ◽  
Dna Lesion ◽  
Nucleotide Incorporation ◽  
Mutagenic Effects ◽  
In Cells

7,8-Dihydro-8-oxoguanine (oxoG) is the most abundant oxidative DNA lesion with dual coding properties. It forms both Watson–Crick (anti)oxoG:(anti)C and Hoogsteen (syn)oxoG:(anti)A base pairs without a significant distortion of a B-DNA helix. DNA polymerases bypass oxoG but the accuracy of nucleotide incorporation opposite the lesion varies depending on the polymerase-specific interactions with the templating oxoG and incoming nucleotides. High-fidelity replicative DNA polymerases read oxoG as a cognate base for A while treating oxoG:C as a mismatch. The mutagenic effects of oxoG in the cell are alleviated by specific systems for DNA repair and nucleotide pool sanitization, preventing mutagenesis from both direct DNA oxidation and oxodGMP incorporation. DNA translesion synthesis could provide an additional protective mechanism against oxoG mutagenesis in cells. Several human DNA polymerases of the X- and Y-families efficiently and accurately incorporate nucleotides opposite oxoG. In this review, we address the mutagenic potential of oxoG in cells and discuss the structural basis for oxoG bypass by different DNA polymerases and the mechanisms of the recognition of oxoG by DNA glycosylases and dNTP hydrolases.

Developing a Genetic System in Deinococcus radiodurans for Analyzing Mutations

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 661-668
Author(s):  
Mandy Kim ◽  
Erika Wolff ◽  
Tiffany Huang ◽  
Lilit Garibyan ◽  
Ashlee M Earl ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Deinococcus Radiodurans ◽  
Genetic System ◽  
Base Change ◽  
Base Substitution ◽  
Wild Type ◽  
Base Pairs ◽  
E Coli ◽  
Radiation Induced ◽  
Induced Mutagenesis

Abstract We have applied a genetic system for analyzing mutations in Escherichia coli to Deinococcus radiodurans, an extremeophile with an astonishingly high resistance to UV- and ionizing-radiation-induced mutagenesis. Taking advantage of the conservation of the β-subunit of RNA polymerase among most prokaryotes, we derived again in D. radiodurans the rpoB/Rif r system that we developed in E. coli to monitor base substitutions, defining 33 base change substitutions at 22 different base pairs. We sequenced >250 mutations leading to Rif r in D. radiodurans derived spontaneously in wild-type and uvrD (mismatch-repair-deficient) backgrounds and after treatment with N-methyl-N′-nitro-N-nitrosoguanidine (NTG) and 5-azacytidine (5AZ). The specificities of NTG and 5AZ in D. radiodurans are the same as those found for E. coli and other organisms. There are prominent base substitution hotspots in rpoB in both D. radiodurans and E. coli. In several cases these are at different points in each organism, even though the DNA sequences surrounding the hotspots and their corresponding sites are very similar in both D. radiodurans and E. coli. In one case the hotspots occur at the same site in both organisms.

scholarly journals Structural basis for the multi-activity factor Rad5 in replication stress tolerance

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Miaomiao Shen ◽  
Nalini Dhingra ◽  
Quan Wang ◽  
Chen Cheng ◽  
Songbiao Zhu ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Ubiquitin Ligase ◽  
Replication Fork ◽  
Replication Stress ◽  
Spatial Arrangement ◽  
Structural Basis ◽  
Dna Lesion ◽  
Activity Factor ◽  
Fork Regression ◽  
New Type

AbstractThe yeast protein Rad5 and its orthologs in other eukaryotes promote replication stress tolerance and cell survival using their multiple activities, including ubiquitin ligase, replication fork remodeling and DNA lesion targeting activities. Here, we present the crystal structure of a nearly full-length Rad5 protein. The structure shows three distinct, but well-connected, domains required for Rad5’s activities. The spatial arrangement of these domains suggest that different domains can have autonomous activities but also undergo intrinsic coordination. Moreover, our structural, biochemical and cellular studies demonstrate that Rad5’s HIRAN domain mediates interactions with the DNA metabolism maestro factor PCNA and contributes to its poly-ubiquitination, binds to DNA and contributes to the Rad5-catalyzed replication fork regression, defining a new type of HIRAN domains with multiple activities. Our work provides a framework to understand how Rad5 integrates its various activities in replication stress tolerance.

Kinetic studies on the reaction of cob(II)alamin with hypochlorous acid: Evidence for one electron oxidation of the metal center and corrin ring destruction

2016 ◽  
Vol 163 ◽  
pp. 81-87 ◽  
Author(s):  
Rohan S. Dassanayake ◽  
Mohamed M. Farhath ◽  
Jacob T. Shelley ◽  
Soumitra Basu ◽  
Nicola E. Brasch
Keyword(s):  
Hypochlorous Acid ◽  
Kinetic Studies ◽  
Metal Center

scholarly journals Comprehensive understanding of acetohydroxyacid synthase inhibition by different herbicide families

2017 ◽  
Vol 114 (7) ◽  
pp. E1091-E1100 ◽  
Author(s):  
Mario D. Garcia ◽  
Amanda Nouwens ◽  
Thierry G. Lonhienne ◽  
Luke W. Guddat
Keyword(s):  
Binding Site ◽  
Crystal Structures ◽  
Kinetic Studies ◽  
Herbicidal Activity ◽  
Structural Basis ◽  
Acetohydroxyacid Synthase ◽  
Branched Chain Amino Acid ◽  
Application Rates ◽  
Herbicide Binding ◽  
Branched Chain

Five commercial herbicide families inhibit acetohydroxyacid synthase (AHAS, E.C. 2.2.1.6), which is the first enzyme in the branched-chain amino acid biosynthesis pathway. The popularity of these herbicides is due to their low application rates, high crop vs. weed selectivity, and low toxicity in animals. Here, we have determined the crystal structures of Arabidopsis thaliana AHAS in complex with two members of the pyrimidinyl-benzoate (PYB) and two members of the sulfonylamino-carbonyl-triazolinone (SCT) herbicide families, revealing the structural basis for their inhibitory activity. Bispyribac, a member of the PYBs, possesses three aromatic rings and these adopt a twisted “S”-shaped conformation when bound to A. thaliana AHAS (AtAHAS) with the pyrimidinyl group inserted deepest into the herbicide binding site. The SCTs bind such that the triazolinone ring is inserted deepest into the herbicide binding site. Both compound classes fill the channel that leads to the active site, thus preventing substrate binding. The crystal structures and mass spectrometry also show that when these herbicides bind, thiamine diphosphate (ThDP) is modified. When the PYBs bind, the thiazolium ring is cleaved, but when the SCTs bind, ThDP is modified to thiamine 2-thiazolone diphosphate. Kinetic studies show that these compounds not only trigger reversible accumulative inhibition of AHAS, but also can induce inhibition linked with ThDP degradation. Here, we describe the features that contribute to the extraordinarily powerful herbicidal activity exhibited by four classes of AHAS inhibitors.

scholarly journals Chemical interactions between ship-originated air pollutants and ocean-emitted halogens

2021 ◽  
Author(s):  
Qinyi Li ◽  
Alba Badia ◽  
Rafael P. Fernandez ◽  
Anoop S. Mahajan ◽  
Ana Isabel López-Noreña ◽  
...  
Keyword(s):  
Air Pollutants ◽  
Atmospheric Composition ◽  
Chemical Transformations ◽  
Chemical Interactions ◽  
China Sea ◽  
Reactive Halogen Species ◽  
The Impact ◽  
Surface Increase ◽  
Halogen Species

<p>Ocean-going ships supply products from one region to another and contribute to the world’s economy. Ship exhaust contains many air pollutants and results in significant changes in marine atmospheric composition. The role of Reactive Halogen Species (RHS) in the troposphere has received increasing recognition and oceans are the largest contributors to their atmospheric burden. However, the impact of shipping emissions on RHS and that of RHS on ship-originated air pollutants have not been studied in detail. Here, an updated WRF-Chem model is utilized to explore the chemical interactions between ship emissions and oceanic RHS over the East Asia seas in summer. The emissions and resulting chemical transformations from shipping activities increase the level of NO and NO<sub>2</sub> at the surface, increase O<sub>3</sub> in the South China Sea, but decrease O<sub>3</sub> in the East China Sea. Such changes in pollutants result in remarkable changes in the levels of RHS as well as in their partitioning. The abundant RHS, in turn, reshape the loadings of air pollutants and those of the oxidants with marked patterns along the ship tracks. We, therefore, suggest that these important chemical interactions of ship-originated emissions with RHS should be considered in the environmental policy assessments of the role of shipping emissions in air quality and climate.</p>

scholarly journals Mechanism of R-loop formation and conformational activation of Cas9

2021 ◽  
Author(s):  
Martin Pacesa ◽  
Martin Jinek
Keyword(s):  
Dna Cleavage ◽  
Structural Basis ◽  
Seed Region ◽  
Loop Formation ◽  
Base Pairs ◽  
Guide Rna ◽  
Target Strand ◽  
Target Dna ◽  
Dna Strand ◽  
Dna Substrate

Cas9 is a CRISPR-associated endonuclease capable of RNA-guided, site-specific DNA cleavage. The programmable activity of Cas9 has been widely utilized for genome editing applications. Despite extensive studies, the precise mechanism of target DNA binding and on-/off-target discrimination remains incompletely understood. Here we report cryo-EM structures of intermediate binding states of Streptococcus pyogenes Cas9 that reveal domain rearrangements induced by R-loop propagation and PAM-distal duplex positioning. At early stages of binding, the Cas9 REC2 and REC3 domains form a positively charged cleft that accommodates the PAM-distal duplex of the DNA substrate. Target hybridisation past the seed region positions the guide-target heteroduplex into the central binding channel and results in a conformational rearrangement of the REC lobe. Extension of the R-loop to 16 base pairs triggers the relocation of the HNH domain towards the target DNA strand in a catalytically incompetent conformation. The structures indicate that incomplete target strand pairing fails to induce the conformational displacements necessary for nuclease domain activation. Our results establish a structural basis for target DNA-dependent activation of Cas9 that advances our understanding of its off-target activity and will facilitate the development of novel Cas9 variants and guide RNA designs with enhanced specificity and activity.

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