scholarly journals Bacteriophage T4 rnh (RNase H) Null Mutations: Effects on Spontaneous Mutation and Epistatic Interaction withrII Mutations

1999 ◽  
Vol 181 (10) ◽  
pp. 3123-3128 ◽  
Author(s):  
Anna Bebenek ◽  
Leslie A. Smith ◽  
John W. Drake
Keyword(s):  
Bacteriophage T4 ◽  
Spontaneous Mutation ◽  
Rnase H ◽  
Plaque Morphology ◽  
Mutation Process ◽  
Mutational Specificity ◽  
Dna Alterations ◽  
Mutator Effect ◽  
The Impact ◽  
Forward Mutation

ABSTRACT The bacteriophage T4 rnh gene encodes T4 RNase H, a relative of a family of flap endonucleases. T4 rnh null mutations reduce burst sizes, increase sensitivity to DNA damage, and increase the frequency of acriflavin resistance (Acr) mutations. Because mutations in the related Saccharomyces cerevisiae RAD27 gene display a remarkable duplication mutator phenotype, we further explored the impact of rnh mutations upon the mutation process. We observed that most Acrmutants in an rnh + strain containac mutations, whereas only roughly half of the Acr mutants detected in an rnhΔ strain bearac mutations. In contrast to the mutational specificity displayed by most mutators, the DNA alterations of acmutations arising in rnhΔ andrnh + backgrounds are indistinguishable. Thus, the increase in Acr mutants in an rnhΔ background is probably not due to a mutator effect. This conclusion is supported by the lack of increase in the frequency of rImutations in an rnhΔ background. In a screen that detects mutations at both the rI locus and the much largerrII locus, the r frequency was severalfold lower in anrnhΔ background. This decrease was due to the phenotype of rnh rII double mutants, which display an r+plaque morphology but retain the characteristic inability ofrII mutants to grow on λ lysogens. Finally, we summarize those aspects of T4 forward-mutation systems which are relevant to optimal choices for investigating quantitative and qualitative aspects of the mutation process.

scholarly journals SPONTANEOUS UNSTABLE UNC-22 IV MUTATIONS IN C. ELEGANS VAR. BERGERAC

Genetics ◽  
1984 ◽  
Vol 108 (4) ◽  
pp. 859-877
Author(s):  
D G Moerman ◽  
R H Waterston
Keyword(s):  
Mutation Frequency ◽  
Spontaneous Mutation ◽  
Phenotypic Effect ◽  
C Elegans ◽  
High Mutation Frequency ◽  
Mutator Activity ◽  
Discrete Site ◽  
Unstable Mutations ◽  
Spontaneous Mutation Frequency ◽  
Forward Mutation

ABSTRACT This paper describes a mutator system in the nematode Caenorhabditis elegans var. Bergerac for the gene unc-22. Of nine C. elegans and two C. briggsae strains tested only the Bergerac BO strain yielded mutant animals at a high frequency and the unc-22 IV gene is a preferred mutational target. The forward spontaneous mutation frequency at the unc-22 locus in Bergerac BO is about 1 × 10-4, and most of these spontaneous unc-22 mutations revert at frequencies between 2 × 10-3 and 2 × 10-4. Both the forward mutation frequency and the reversion frequency are sensitive to genetic background. Spontaneous unc-22 mutations derived in a Bergerac background and placed in a primarily Bristol background revert at frequencies of <10-6. When reintroduced into a Bergerac/Bristol hybrid background the mutations once again become unstable. The mutator activity could not be localized to a discrete site in the Bergerac genome. Nor did mutator activity require the Bergerac unc-22 gene as a target since the Bristol unc-22 homolog placed in a Bergerac background also showed high mutation frequency. Intragenic mapping of two spontaneous unc-22 alleles, st136 and st137, place both mutations in the central region of the known unc-22 map. However, these mutations probably recombine with one another, suggesting that the unstable mutations can occur in more than one site in unc-22. Examination of the phenotypic effect of these mutations on muscle structure indicates that they are less severe in their effect than a known amber allele. We suggest that this mutator system is polygenic and dispersed over the nematode genome and could represent activity of the transposable element Tc1.

scholarly journals Genetic evidence for two protein domains and a potential new activity in bacteriophage T4 DNA polymerase.

Genetics ◽  
1990 ◽  
Vol 124 (2) ◽  
pp. 213-220 ◽  
Author(s):  
L J Reha-Krantz
Keyword(s):  
Dna Polymerase ◽  
Bacteriophage T4 ◽  
Rnase H ◽  
Ribonuclease H ◽  
Temperature Sensitive ◽  
Polymerase Gene ◽  
Dna Polymerase I ◽  
E Coli ◽  
Intragenic Complementation ◽  
Polymerase I

Abstract Intragenic complementation was detected within the bacteriophage T4 DNA polymerase gene. Complementation was observed between specific amino (N)-terminal, temperature-sensitive (ts) mutator mutants and more carboxy (C)-terminal mutants lacking DNA polymerase polymerizing functions. Protein sequences surrounding N-terminal mutation sites are similar to sequences found in Escherichia coli ribonuclease H (RNase H) and in the 5'----3' exonuclease domain of E. coli DNA polymerase I. These observations suggest that T4 DNA polymerase, like E. coli DNA polymerase I, contains a discrete N-terminal domain.

scholarly journals Effects of the W153L Substitution in HIV Reverse Transcriptase on Viral Replication and Drug Resistance to Multiple Categories of Reverse Transcriptase Inhibitors

2014 ◽  
Vol 58 (8) ◽  
pp. 4515-4526 ◽  
Author(s):  
Hong-Tao Xu ◽  
Susan P. Colby-Germinario ◽  
Maureen Oliveira ◽  
Daniel Rajotte ◽  
Richard Bethell ◽  
...  
Keyword(s):  
Viral Replication ◽  
Reverse Transcriptase ◽  
Rnase H ◽  
Hiv Reverse Transcriptase ◽  
Compound A ◽  
Enzymatic Function ◽  
Biochemical Assays ◽  
Rt Inhibitors ◽  
The Impact ◽  
Hiv 1

ABSTRACTA W153L substitution in HIV-1 reverse transcriptase (RT) was recently identified by selection with a novel nucleotide-competing RT inhibitor (NcRTI) termed compound A that is a member of the benzo[4,5]furo[3,2,d]pyrimidin-2-one NcRTI family of drugs. To investigate the impact of W153L, alone or in combination with the clinically relevant RT resistance substitutions K65R (change of Lys to Arg at position 65), M184I, K101E, K103N, E138K, and Y181C, on HIV-1 phenotypic susceptibility, viral replication, and RT enzymatic function, we generated recombinant RT enzymes and viruses containing each of these substitutions or various combinations of them. We found that W153L-containing viruses were impaired in viral replicative capacity and were hypersusceptible to tenofovir (TFV) while retaining susceptibility to most nonnucleoside RT inhibitors. The nucleoside 3TC retained potency against W153L-containing viruses but not when the M184I substitution was also present. W153L was also able to reverse the effects of the K65R substitution on resistance to TFV, and K65R conferred hypersusceptibility to compound A. Biochemical assays demonstrated that W153L alone or in combination with K65R, M184I, K101E, K103N, E138K, and Y181C impaired enzyme processivity and polymerization efficiency but did not diminish RNase H activity, providing mechanistic insights into the low replicative fitness associated with these substitutions. We show that the mechanism of the TFV hypersusceptibility conferred by W153L is mainly due to increased efficiency of TFV-diphosphate incorporation. These results demonstrate that compound A and/or derivatives thereof have the potential to be important antiretroviral agents that may be combined with tenofovir to achieve synergistic results.

Abstract 5772: The Impact of Aortic Plaque Morphology on Survival Rate and the Incidence of Subsequent Embolic Event: Very Long-Term Follow-Up Data

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Chisato Izumi ◽  
Shuichi Takahashi ◽  
Sumiyo Hashiwada ◽  
Koji Hanazawa ◽  
Jiro Sakamoto ◽  
...  
Keyword(s):  
Survival Rate ◽  
Event Rate ◽  
Plaque Morphology ◽  
Embolic Event ◽  
Aortic Plaque ◽  
Long Term Follow Up ◽  
The Impact ◽  
The Relationship

Atheromatous plaques of the aorta have been regarded as a potential source of emboli, but there are few reports about the frequency and prognosis of patients with thoracic aortic plaques and about the relationship between plaque morphology and prognosis, especially long-term follow-up data. The purpose of this study is to clarify the impact of aortic atheromatous plaque morphology on survival rate and the incidence of subsequent embolic event. We retrospectively investigated 1570 consecutive patients who underwent transesophageal echocardiography between 1991 and 2003. The presence of severe plaque (>5mm in thickness) in the thoracic aorta were examined. Survival rate and subsequent embolic event rate were compared between patients with severe plaque and 109 control patients. The control patients were selected from the patients who showed no or mild plaque and as they were matched for age, gender, and risk factors of atherosclerosis with the patients with severe aortic plaque. The relationship between aortic plaque morphology and prognosis was also estimated, according to the presence of ulceration, calcification, hypoechoic plaques, and mobile plaques. Mean follow-up period was 8.7 years. Among 1570 patients, severe aortic plaque was detected in 92 patients (5.9%). These 92 patients showed significantly low survival rate and high subsequent embolic event rate compared with control patients (8-year survival rate, 50% vs 87%, 8-year embolic event free rate, 57% vs 90%). The relative risk of death was significantly increased for ulceration (2.4, 95% CI;1.1–5.2) and the relative risk of embolic events was significantly increased for mobile plaques (2.2, 95% CI;1.1–5.1). In conclusion, aortic plaque > 5mm in thickness was a predictor of a low survival rate and a high embolic event rate. Among patients with aortic plaque >5mm in thickness, ulceration was a predictor of a low survival rate and mobile plaque was a predictor of a high embolic event rate.

scholarly journals The Relationship between Coronary Artery Wall Shear Strain and Plaque Morphology: A Systematic Review and Meta-Analysis

Diagnostics ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 91 ◽  
Author(s):  
Artan Bajraktari ◽  
Ibadete Bytyçi ◽  
Michael Y. Henein
Keyword(s):  
Coronary Artery ◽  
Shear Strain ◽  
Meta Analysis ◽  
Calcium Score ◽  
Necrotic Core ◽  
Plaque Burden ◽  
Plaque Morphology ◽  
Wall Shear ◽  
The Impact ◽  
The Relationship

Background and Aim: Arterial wall shear strain (WSS) has been proposed to impact the features of atherosclerotic plaques. The aim of this meta-analysis was to assess the impact of different types of WSS on plaque features in coronary artery disease (CAD). Methods: We systematically searched PubMed-Medline, EMBASE, Scopus, Google Scholar, and the Cochrane Central Registry, from 1989 up to January 2020 and selected clinical trials and observational studies which assessed the relationship between WSS, measured by intravascular ultrasound (IVUS), and plaque morphology in patients with CAD. Results: In four studies, a total of 72 patients with 13,098 coronary artery segments were recruited, with mean age 57.5 ± 9.5 years. The pooled analysis showed that low WSS was associated with larger baseline lumen area (WMD 2.55 [1.34 to 3.76, p < 0.001]), smaller plaque area (WMD −1.16 [−1.84 to −0.49, p = 0.0007]), lower plaque burden (WMD −12.7 [−21.4 to −4.01, p = 0.04]), and lower necrotic core area (WMD −0.32 [−0.78 to 0.14, p = 0.04]). Low WSS also had smaller fibrous area (WMD −0.79 [−1.88 to 0.30, p = 0.02]) and smaller fibro-fatty area (WMD −0.22 [−0.57 to 0.13, p = 0.02]), compared with high WSS, but the dense calcium score was similar between the two groups (WMD −0.17 [−0.47 to 0.13, p = 0.26]). No differences were found between intermediate and high WSS. Conclusions: High WSS is associated with signs of plaque instability such as higher necrotic core, higher calcium score, and higher plaque burden compared with low WSS. These findings highlight the role of IVUS in assessing plaque vulnerability.

DNA spontaneous mutation and its role in the evolution of GC-content: assessing the impact of the genetic sequence

2015 ◽  
Vol 17 (12) ◽  
pp. 7754-7760 ◽  
Author(s):  
José P. Cerón-Carrasco ◽  
Denis Jacquemin
Keyword(s):  
Dna Sequence ◽  
Base Pair ◽  
Spontaneous Mutation ◽  
Gc Content ◽  
Genetic Sequence ◽  
The Impact

We use theoretical tools to investigate the possible role played by a DNA sequence in the base pair tautomerization phenomena.

scholarly journals Substitutions in Bacteriophage T4 AsiA andEscherichia coli ς70 That Suppress T4motA Activation Mutations

2001 ◽  
Vol 183 (7) ◽  
pp. 2289-2297 ◽  
Author(s):  
Marco P. Cicero ◽  
Meghan M. Sharp ◽  
Carol A. Gross ◽  
Kenneth N. Kreuzer
Keyword(s):  
Rna Polymerase ◽  
Burst Size ◽  
Bacteriophage T4 ◽  
In Vitro Transcription ◽  
Positive Control ◽  
Plaque Morphology ◽  
Mutant Proteins ◽  
E Coli

ABSTRACT Bacteriophage T4 middle-mode transcription requires two phage-encoded proteins, the MotA transcription factor and AsiA coactivator, along with Escherichia coli RNA polymerase holoenzyme containing the ς70 subunit. AmotA positive control (pc) mutant, motA-pc1, was used to select for suppressor mutations that alter other proteins in the transcription complex. Separate genetic selections isolated two AsiA mutants (S22F and Q51E) and five ς70 mutants (Y571C, Y571H, D570N, L595P, and S604P). All seven suppressor mutants gave partial suppressor phenotypes in vivo as judged by plaque morphology and burst size measurements. The S22F mutant AsiA protein and glutathione S-transferase fusions of the five mutant ς70 proteins were purified. All of these mutant proteins allowed normal levels of in vitro transcription when tested with wild-type MotA protein, but they failed to suppress the mutant MotA-pc1 protein in the same assay. The ς70 substitutions affected the 4.2 region, which binds the −35 sequence of E. coli promoters. In the presence of E. coli RNA polymerase without T4 proteins, the L595P and S604P substitutions greatly decreased transcription from standard E. colipromoters. This defect could not be explained solely by a disruption in −35 recognition since similar results were obtained with extended −10 promoters. The generalized transcriptional defect of these two mutants correlated with a defect in binding to core RNA polymerase, as judged by immunoprecipitation analysis. The L595P mutant, which was the most defective for in vitro transcription, failed to support E. coli growth.

scholarly journals Rapid evolution by spontaneous mutation increases genetic diversity facilitating plant population survival

2018 ◽  
Author(s):  
Henning Nottebrock ◽  
Mao-Lun Weng ◽  
Matthew T Rutter ◽  
Charles B. Fenster
Keyword(s):  
Large Scale ◽  
Community Dynamics ◽  
Spontaneous Mutation ◽  
Rapid Evolution ◽  
Potential Effect ◽  
Small Scale ◽  
Negative Effects ◽  
Population Survival ◽  
Population And Community Dynamics ◽  
The Impact

Using a mechanistic eco-evolutionary trait-based neighborhood-model, we quantify the impact of mutations on spatial interactions to better understand the potential effect of niche evolution through mutations on the population dynamics of Arabidopsis thaliana. We use 100 twenty-fifth generation mutation accumulation (MA) lines (genotypes) derived from one founder genotype to study mutational effects on neighbor responses in a field experiment. We created individual-based maps (15,000 individuals), including phenotypic variation, to quantify mutational effects within genotypes versus between genotypes on reproduction and survival. At small-scale, survival is enhanced but reproduction is decreased when a genotype is surrounded by different genotypes. At large-scale, seed set is facilitated by different genotypes while the same genotype has either no effect or negative effects. Mutations may provide a mechanism for plants to quickly evolve niches and may drive competition, facilitation and selection with profound consequences for future population and community dynamics.

Is there a genomic fingerprint of Radon (Rn)-induced lung cancer (LC)? Comparison of genomic alterations in LC specimens from high and low Rn zones.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 1572-1572
Author(s):  
Hina Khan ◽  
Harish Saiganesh ◽  
Adam J. Olszewski ◽  
Yasmine Baca ◽  
Michaela Kastura ◽  
...  
Keyword(s):  
Dna Repair ◽  
Rhode Island ◽  
Validation Cohort ◽  
Alpha Particles ◽  
Tobacco Smoke Exposure ◽  
Lung Carcinogenesis ◽  
The Us ◽  
Dna Alterations ◽  
Genomic Fingerprint ◽  
The Impact

1572 Background: Rn-222 is a radioactive gas found in rocks and soil. It emits alpha particles that cause dsDNA breaks and increase potential for carcinogenesis. Rn is the 2nd leading cause of LC in the US after smoking. EPA estimates >15,000 deaths/yr (9% of LC deaths) from Rn. We hypothesize that the impact of Rn exposure may be reflected in LC gene mutation (mut) profiles. Methods: Using commercial NGS assays, we retrospectively analyzed genomic DNA alterations in FFPE specimens from 159 LC patients (pts) from the Lifespan Cancer Institute in Rhode Island (2014- 2019), followed by validation in a larger cohort of 5,532 pts using Caris platform. Based on EPA Rn maps, we identified counties with high indoor Rn levels (>4 pci/L; HR), and compared gene mut patterns with those from low Rn zones (<4 pci/L; LR). Based on pt’s zip code of residence, we categorized them to HR and LR. In the validation cohort, p values adjusted for multiple comparison (q) of < .05 were considered significant. Results: In the pilot cohort, 35 pts (22%) were in HR and 124 (78%) in LR zones. Adenocarcinoma histology was most frequent (73%) and smoking prevalence was high (75%) in both groups. Most prevalent alterations were TP53, KRAS and CDKN2A muts. In the HR, we noted more frequent recurrent muts in 2 DNA repair genes (DDR): ATM (11 vs 1%, p= .00086) and CHEK2 (6 vs 0%, p= .047) when compared to LR group. When classified into major pathways implicated in lung carcinogenesis, higher frequency of mutations were seen in DDR in HR zones vs. LR (29 vs 13%, p= .038). In the validation cohort, 1,433 (26%) pts were in HR and 4099 (74%) in LR zones. Among the DDR genes, ATM muts in HR group tended to be more frequent (4.7 vs 3.4% in LR, p= .03) as well as PALB2 (0.9 vs 0.4%, p= .02) while no difference seen in CHEK2. Other genes with significantly higher prevalence in HR were TP53, SMARCA4 and NFE2L2 (q< .05); while KMT2D, KEAP1, CDKN2A, MET, NF2, DNMT3A, CCND1 and FAS show a trend (p< .05). EGFR muts were significantly more frequent in LR zones (8.4 vs 14.6%, q= .001). Similar to the pilot cohort, DDR pathway alterations trend to be higher in HR zones (14 vs 12%, p= .05). Using a high TMB cut-off >10, tumors from HR zones had significantly higher TMB when compared to LR zones (56 vs 48%, q= .0005). Conclusions: To our knowledge, this is the first attempt to elucidate the pathobiology of Rn induced LC using gene mut analyses. Our observations suggest that LC associated with higher Rn exposure may have disabled DNA repair pathways and higher TMB. Assuming uniform tobacco smoke exposure, higher Rn was not associated with EGFR mut.

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