Integration of the pSLT Plasmid into the Salmonella Chromosome Results in a Temperature-Sensitive Growth Defect Due to Aberrant DNA Replication

ABSTRACT A mutant of Salmonella enterica serovar Typhimurium was isolated that simultaneously affected two metabolic pathways as follows: NAD metabolism and DNA repair. The mutant was isolated as resistant to a nicotinamide analog and as temperature-sensitive for growth on minimal glucose medium. In this mutant, Salmonella's 94-kb virulence plasmid pSLT had recombined into the chromosome upstream of the NAD salvage pathway gene pncA. This insertion blocked most transcription of pncA, which reduced uptake of the nicotinamide analog. The pSLT insertion mutant also exhibited phenotypes associated with induction of the SOS DNA repair system, including an increase in filamentous cells, higher exonuclease III and catalase activities, and derepression of SOS gene expression. Genome sequencing revealed increased read coverage extending out from the site of pSLT insertion. The two pSLT replication origins are likely initiating replication of the chromosome near the normal replication terminus. Too much replication initiation at the wrong site is probably causing the observed growth defects. Accordingly, deletion of both pSLT replication origins restored growth at higher temperatures. IMPORTANCE In studies that insert a second replication origin into the chromosome, both origins are typically active at the same time. In contrast, the integrated pSLT plasmid initiated replication in stationary phase after normal chromosomal replication had finished. The gradient in read coverage extending out from a single site could be a simple but powerful tool for studying replication and detecting chromosomal rearrangements. This technique may be of particular value when a genome has been sequenced for the first time to verify correct assembly.

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The Virulence Plasmid-Encoded impCAB Operon Enhances Survival and Induced Mutagenesis in Shigella flexneriafter Exposure to UV Radiation

Infection and Immunity ◽

10.1128/iai.67.3.1415-1423.1999 ◽

1999 ◽

Vol 67 (3) ◽

pp. 1415-1423 ◽

Cited By ~ 43

Author(s):

Laura J. Runyen-Janecky ◽

Mei Hong ◽

Shelley M. Payne

Keyword(s):

Escherichia Coli ◽

Dna Repair ◽

Nucleotide Sequence ◽

Uv Radiation ◽

Uv Irradiation ◽

Shigella Flexneri ◽

Virulence Plasmid ◽

Repair System ◽

Induced Mutagenesis ◽

Dna Fragment

ABSTRACT Upon exposure to UV radiation, Shigella flexneri SA100 displayed survival and mutation frequencies comparable to those ofEscherichia coli AB1157, which contains a functional UmuDC error-prone DNA repair system. Survival of SA100 after UV irradiation was associated with the presence of the 220-kb virulence plasmid, pVP. This plasmid encodes homologues of ImpA and ImpB, which comprise an error-prone DNA repair system encoded on plasmid TP110 that was initially identified in Salmonella typhimurium, and ImpC, encoded upstream of ImpA and ImpB. Although the impBgene was present in representatives of all four species ofShigella, not all isolates tested contained the gene.Shigella isolates that lacked impB were more sensitive to UV radiation than isolates that containedimpB. The nucleotide sequence of a 2.4-kb DNA fragment containing the imp operon from S. flexneri SA100 pVP was 96% identical to the impoperon from the plasmid TP110. An SA100 derivative with a mutation in the impB gene had reduced survival following UV irradiation and less UV-induced mutagenesis relative to the parental strain. We also found that S. flexneri contained a chromosomally encoded umuDC operon; however, theumuDC promoter was not induced by exposure to UV radiation. This suggests that the imp operon but not theumuDC operon contributes to survival and induced mutagenesis in S. flexneri following exposure to UV radiation.

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EFFECT OF ARYL HYDROCARBON RECEPTOR AGONISTS AND LIPOPOLYSACCHARIDE ON BENZO(A)PYRENE GENOTOXICITY MARKERS

Токсикологический вестник ◽

10.36946/0869-7922-2019-3-19-25 ◽

2019 ◽

pp. 19-25 ◽

Cited By ~ 1

Author(s):

V. N. Babakov ◽

N. Yu. Rogovskaya ◽

I. D. Kurdyukov ◽

P. P. Beltyukov ◽

S. A. Dulov ◽

...

Keyword(s):

Dna Repair ◽

Aryl Hydrocarbon Receptor ◽

P53 Protein ◽

Control Level ◽

Repair System ◽

Human Hepatoma Cells ◽

Kinase Activation ◽

Receptor Agonists ◽

Checkpoint Kinases ◽

Aryl Hydrocarbon

The effect of aryl hydrocarbon receptor agonists (FICZ and ITE), as well as lipopolysaccharide under the toxic action of benzo(a)pyrene in HepaRG human hepatoma cells was evaluated. Active forms of the key stress-activated kinase cascades and DNA repair system proteins were used as markers of the genotoxic action of benzo(a)pyrene. A mixture of lipopolysaccharide with benzo(a)pyrene increases benzo(a)pyrene cytotoxicity and reduces the activation of DNA repair system proteins below the control level. Aryl hydrocarbon receptor agonists (FICZ and ITE) exhibit a cytoprotective effect against benzo(a) pyrene, enhance Akt1 kinase activation, and downregulate activation of the p53 protein and Chk1 and Chk2 checkpoint kinases. Thus, FICZ and ITE reduce the genotoxicity of benzo(a)pyrene.

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Temperature-sensitive DNA repair mutations in the cellular slime mould Dictyostelium discoideum

Current Genetics ◽

10.1007/bf00429818 ◽

1981 ◽

Vol 3 (3) ◽

pp. 167-171 ◽

Cited By ~ 2

Author(s):

Dennis L. Welker ◽

Keith L. Williams

Keyword(s):

Dna Repair ◽

Dictyostelium Discoideum ◽

Temperature Sensitive ◽

Cellular Slime Mould ◽

Slime Mould ◽

Cellular Slime

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Exploring the multiple roles of guardian of the genome: P53

Egyptian Journal of Medical Human Genetics ◽

10.1186/s43042-020-00089-x ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Wasim Feroz ◽

Arwah Mohammad Ali Sheikh

Keyword(s):

Cell Cycle ◽

Dna Repair ◽

Crucial Role ◽

Cellular Response ◽

Genotoxic Stress ◽

Specific Response ◽

Main Body ◽

Repair System ◽

Tumour Suppression

Abstract Background Cells have evolved balanced mechanisms to protect themselves by initiating a specific response to a variety of stress. The TP53 gene, encoding P53 protein, is one of the many widely studied genes in human cells owing to its multifaceted functions and complex dynamics. The tumour-suppressing activity of P53 plays a principal role in the cellular response to stress. The majority of the human cancer cells exhibit the inactivation of the P53 pathway. In this review, we discuss the recent advancements in P53 research with particular focus on the role of P53 in DNA damage responses, apoptosis, autophagy, and cellular metabolism. We also discussed important P53-reactivation strategies that can play a crucial role in cancer therapy and the role of P53 in various diseases. Main body We used electronic databases like PubMed and Google Scholar for literature search. In response to a variety of cellular stress such as genotoxic stress, ischemic stress, oncogenic expression, P53 acts as a sensor, and suppresses tumour development by promoting cell death or permanent inhibition of cell proliferation. It controls several genes that play a role in the arrest of the cell cycle, cellular senescence, DNA repair system, and apoptosis. P53 plays a crucial role in supporting DNA repair by arresting the cell cycle to purchase time for the repair system to restore genome stability. Apoptosis is essential for maintaining tissue homeostasis and tumour suppression. P53 can induce apoptosis in a genetically unstable cell by interacting with many pro-apoptotic and anti-apoptotic factors. Furthermore, P53 can activate autophagy, which also plays a role in tumour suppression. P53 also regulates many metabolic pathways of glucose, lipid, and amino acid metabolism. Thus under mild metabolic stress, P53 contributes to the cell’s ability to adapt to and survive the stress. Conclusion These multiple levels of regulation enable P53 to perform diversified roles in many cell responses. Understanding the complete function of P53 is still a work in progress because of the inherent complexity involved in between P53 and its target proteins. Further research is required to unravel the mystery of this Guardian of the genome “TP53”.

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Isolation of a Schizosaccharomyces pombe rad21ts Mutant That Is Aberrant in Chromosome Segregation, Microtubule Function, DNA Repair and Sensitive to Hydroxyurea: Possible Involvement of Rad21 in Ubiquitin-Mediated Proteolysis

Genetics ◽

10.1093/genetics/148.1.49 ◽

1998 ◽

Vol 148 (1) ◽

pp. 49-57

Author(s):

Kazuo Tatebayashi ◽

Jun-ichi Kato ◽

Hideo Ikeda

Keyword(s):

Dna Repair ◽

Temperature Sensitive ◽

Permissive Temperature ◽

Repair Gene ◽

Tubulin Genes ◽

Gene Coding ◽

Abnormal Mitosis ◽

Dna Repair Gene ◽

Nuclear Structures ◽

Microtubule Function

Abstract The fission yeast DNA repair gene rad21+ is essential for cell growth. To investigate the function essential for cell proliferation, we have isolated a temperature-sensitive mutant of the rad21+ gene. The mutant, rad21-K1, showed abnormal mitosis at the nonpermissive temperature. Some cells contained abnormal nuclear structures, such as condensed chromosomes with short spindles, or chromosomes stretched or unequally separated by elongating spindles. Other cells exhibited the displaced nucleus or a cut-like phenotype. Similar abnormalities were observed when the Rad21 protein was depleted from cells. We therefore concluded that Rad21 is essential for proper segregation of chromosomes. Moreover, the rad21-K1 mutant is sensitive not only to UV and γ-ray irradiation but to thiabendazole and hydroxyurea, indicating that Rad21 plays important roles in microtubule function, DNA repair, and S phase function. The relation to the microtubule function was further confirmed by the fact that rad21+ genetically interacts with tubulin genes, nda2+ and nda3+. Finally, the growth of the rad21-K1 mutant was inhibited at the permissive temperature by introduction of another mutation in the cut9+ gene, coding for a component of the 20S cyclosome/anaphase promoting complex, which is involved in ubiquitin-mediated proteolysis. The results suggest that these diverse functions of Rad21 may be facilitated through ubiquitin-mediated proteolysis.

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Molecular Mechanisms of the Whole DNA Repair System: A Comparison of Bacterial and Eukaryotic Systems

Journal of Nucleic Acids ◽

10.4061/2010/179594 ◽

2010 ◽

Vol 2010 ◽

pp. 1-32 ◽

Cited By ~ 45

Author(s):

Rihito Morita ◽

Shuhei Nakane ◽

Atsuhiro Shimada ◽

Masao Inoue ◽

Hitoshi Iino ◽

...

Keyword(s):

Dna Repair ◽

Molecular Mechanisms ◽

Excision Repair ◽

Thermus Thermophilus ◽

Repair System ◽

System A ◽

Recombination Repair ◽

Repair Mechanisms ◽

Repair Pathways ◽

Base Excision

DNA is subjected to many endogenous and exogenous damages. All organisms have developed a complex network of DNA repair mechanisms. A variety of different DNA repair pathways have been reported: direct reversal, base excision repair, nucleotide excision repair, mismatch repair, and recombination repair pathways. Recent studies of the fundamental mechanisms for DNA repair processes have revealed a complexity beyond that initially expected, with inter- and intrapathway complementation as well as functional interactions between proteins involved in repair pathways. In this paper we give a broad overview of the whole DNA repair system and focus on the molecular basis of the repair machineries, particularly inThermus thermophilusHB8.

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Analysis of pCU1 replication origins: dependence of oriS on the plasmid-encoded replication initiation protein RepA

Plasmid ◽

10.1016/s0147-619x(02)00151-8 ◽

2003 ◽

Vol 49 (2) ◽

pp. 152-159 ◽

Cited By ~ 1

Author(s):

O.P Zoueva ◽

V.N Iyer ◽

T.I Matula ◽

M Kozlowski

Keyword(s):

Replication Initiation ◽

Replication Origins ◽

Replication Initiation Protein

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DNA Repair Gene Expression Adjusted by the PCNA Metagene Predicts Survival in Multiple Cancers

10.20944/preprints201902.0042.v1 ◽

2019 ◽

Author(s):

Leif Peterson ◽

Tatiana Kovyrshina

Keyword(s):

Gene Expression ◽

Dna Repair ◽

Gene Selection ◽

P Value ◽

Survival Prediction ◽

Dna Repair Genes ◽

Repair Gene ◽

A Genome ◽

Dna Repair Gene ◽

Repair Genes

Removal of the proliferation component of gene expression by PCNA adjustment has been addressed in numerous survival prediction studies for breast cancer and all cancers in the TCGA. These studies indicate that widespread co-regulation of proliferation upwardly biases survival prediction when gene selection is performed on a genome-wide basis. In addition, removal of the correlative effects of proliferation does not reduce the random bias associated with survival prediction using random gene selection. Since most cancers become addicted to DNA repair as a result of forced cellular replication, increased oxidation, and repair deficiencies from oncogenic loss or genetic polymorphisms, we pursued an investigation to remove the proliferation component of expression in DNA repair genes to determine survival prediction. This translational hypothesis-driven focus on DNA repair genes is directly amenable to finding new sets of DNA repair genes that could potentially be studied for inhibition therapy. Overall survival (OS) prediction was evaluated in 18 cancers by using normalized RNA-Seq data for 126 DNA repair genes with expression available in TCGA. Transformations for normality and adjustments for age at diagnosis, stage, and PCNA metagene expression were performed for all DNA repair genes. We also analyzed genomic event rates (GER) for somatic mutations, deletions, and amplification in driver genes and DNA repair genes. After performing empirical p-value testing with use of randomly selected gene sets, it was observed that OS could be predicted significantly by sets of DNA repair genes for 61% (11/18) of the cancers. Interestingly, PARP1 was not a significant predictor of survival for any of the 11 cancers. Results from cluster analysis of GERs indicates that the most opportunistic cancers for inhibition therapy may be AML, colorectal, and renal papillary, because of potentially less confounding due to lower GERs for mutations, deletions, and amplifications in DNA repair genes. However, the most opportunistic cancer for inhibition therapy is likely to be AML, since it showed the lowest GERs for mutations, deletions, and amplifications in DNA repair genes. In conclusion, our hypothesis-driven focus to target DNA repair gene expression adjusted for the PCNA metagene as a means of predicting OS in various cancers resulted in statistically significant sets of genes.

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Arabidopsis Mediator subunit 17 connects transcription with DNA repair after UV-B exposure

10.1101/2021.08.02.454780 ◽

2021 ◽

Author(s):

Marisol Giustozzi ◽

Santiago Freytes ◽

Aime Jaskolowski ◽

Micaela Lichy ◽

Julieta L. Mateos ◽

...

Keyword(s):

Dna Damage ◽

Dna Repair ◽

Transcription Initiation ◽

Plant Responses ◽

Repair System ◽

Root Tips ◽

Direct Role ◽

Altered Expression ◽

Eukaryotic Organisms

Mediator 17 (MED17) is a subunit of the Mediator complex that regulates transcription initiation in eukaryotic organisms. In yeast and humans, MED17 also participates in DNA repair, physically interacting with proteins of the Nucleotide Excision DNA Repair system. We here analyzed the role of MED17 in Arabidopsis plants exposed to UV-B radiation, which role has not been previously described. Comparison of med17 mutant transcriptome to that of WT plants showed that almost one third of transcripts with altered expression in med17 plants are also changed by UV-B exposure in WT plants. To validate the role of MED17 in UV-B irradiated plants, plant responses to UV-B were analyzed, including flowering time, DNA damage accumulation and programmed cell death in the meristematic cells of the root tips. Our results show that med17 and OE MED17 plants have altered responses to UV-B; and that MED17 participates in various aspects of the DNA damage response (DDR). Increased sensitivity to DDR after UV-B in med17 plants can be due to altered regulation of UV-B responsive transcripts; but additionally MED17 physically interacts with DNA repair proteins, suggesting a direct role of this Mediator subunit during repair. Finally, we here also show that MED17 is necessary to regulate the DDR activated by ATR, and that PDCD5 overexpression reverts the deficiencies in DDR shown in med17 mutants. Together, the data presented demonstrates that MED17 is an important regulator of the DDR after UV-B radiation in Arabidopsis plants.

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