DNA replication meets genetic exchange: Chromosomal damage and its repair by homologous recombination

Kuzminov, Andrei

doi:10.1073/pnas.151260698

Cited by 198 publications

(131 citation statements)

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“…45 Furthermore, strand breaks can be induced if the replication fork is stalled because of a block in template DNA. 46 Whether the apoptosis observed in our experiments is a general problem associated with the presence of large amounts of oligonucleotides in cells, whether it is a more specific process related to cells that have undergone sequence conversion and whether any of the above mechanisms account for the observed selective apoptosis is currently under investigation. Given that the observed apoptosis appears at 4-6 days after transfection, it will not have influence on the general toxicity parameters that were measured 1 day after transfection.…”

Section: Branched Oligonucleotides Induce Mutated Egfp Reportermentioning

confidence: 90%

“…It has been demonstrated that transfection of cells with ss DNA induces G1 arrest and apoptois. [42][43][44] It is also known that cells stop replicating and enter apoptosis when unrepaired ds breaks accumulate. 45 Furthermore, strand breaks can be induced if the replication fork is stalled because of a block in template DNA.…”

Section: Branched Oligonucleotides Induce Mutated Egfp Reportermentioning

confidence: 99%

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Branched oligonucleotides induce in vivo gene conversion of a mutated EGFP reporter

Olsen¹,

McKeen

Krauß³

2003

Gene Ther

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UKBranched oligonucleotides (b-oligonucleotides) based on a novel branching monomer were used for site-specific sequence alteration in vivo. With a stable integrated mutated enhanced green fluorescent protein (EGFP) template in Chinese hamster ovary cells, up to 0.1% EGFP-positive cells were counted after transfection with b-oligonucleotides. The presence of EGFP protein in converted cells was demonstrated by anti-EGFP immunocytochemistry. Genomic sequencing of converted cells showed in 40% of the analysed clones the corrected wild-type codon, while 9.3% of the sequences showed a corrected wild-type sequence and an additional collateral mutation. Despite the stable corrected genomic locus, converted cells entered selective apoptosis after 3-6 days. The cell line Irs-1 that is deficient in the homologous recombination pathway showed a reduced frequency of boligonucleotide-induced site-specific sequence conversion. The reduced conversion rates in the mutant cell line could be partly rescued by complementation with XRCC2 cDNA.

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Section: Branched Oligonucleotides Induce Mutated Egfp Reportermentioning

confidence: 90%

Section: Branched Oligonucleotides Induce Mutated Egfp Reportermentioning

confidence: 99%

Branched oligonucleotides induce in vivo gene conversion of a mutated EGFP reporter

Olsen¹,

McKeen

Krauß³

2003

Gene Ther

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“…E-mail: slusetti@nmsu.edu. 2 The abbreviations used are: DSB, DNA double-stranded break; ssDNA, single-stranded DNA; dsDNA, double-stranded DNA; ATP␥S, adenosine 5Ј-O-(thiotriphosphate); DTT, dithiothreitol; AEBSF-HCl, 4-(2-aminoethyl)benzenesulfonyl fluoride hydrochloride. …”

mentioning

confidence: 99%

RecN Is a Cohesin-like Protein That Stimulates Intermolecular DNA Interactions in Vitro

Reyes

Patidar

Uranga

et al. 2010

Journal of Biological Chemistry

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The bacterial RecN protein is involved in the recombinational repair of DNA double-stranded breaks, and recN mutants are sensitive to DNA-damaging agents. Little is known about the biochemical function of RecN. Protein sequence analysis suggests that RecN is related to the SMC (structural maintenance of chromosomes) family of proteins, predicting globular N-and C-terminal domains connected by an extensive coil-coiled domain. The N-and C-domains contain the nucleotide-binding sequences Walker A and Walker B, respectively. We have purified the RecN protein from Deinococcus radiodurans and characterized its DNA-dependent and DNA-independent ATPase activity. The cellular genome maintenance processes of DNA replication, recombination, and repair are highly interconnected, sharing multiple pathways and common enzymes. A physical understanding of the function of key enzymes involved in genome maintenance processes is critical for elucidating the basic DNA metabolic strategies of cells. The primary function of homologous DNA recombination in mitotic cells as well as bacterial cells is the nonmutagenic repair of replication forks that have stalled or collapsed at noncoding lesions or breaks (1-3). When a replication fork encounters a break in the phosphodiester backbone of one template strand, a double-stranded break (DSB) 2 results (4). Recombinational DSB repair pathways promote strand invasion to regenerate a fork structure. In Escherichia coli, these pathways include the helicase and nuclease functions of the RecBCD complex, and the RecA protein. RecN, among various other proteins, is required for DSB repair in bacteria. Existing DSB repair models do not encompass RecN, because no clear function has been ascribed to the protein as yet.The recN gene of E. coli (also known as radB (5)) was identified by two groups over 20 years ago. Lloyd et al. (6) isolated a mutation (rec-259) that caused increased sensitivity to UV light in a recBC sbcB background. Independently, Sargentini and Smith (7) isolated the radB101 mutation, which caused sensitivity to ␥-irradiation and mitomycin C. Expression of the recN gene is regulated by the LexA repressor (8, 9), and the RecN protein is one of the most abundantly produced proteins induced as part of the SOS response to DNA damage (10). Once produced in response to damage, RecN protein has a very short half-life (ϳ10 min), because it apparently is rapidly proteolyzed by the ClpXP protease system (11).The recN gene product was originally placed in the RecF-dependent gap repair pathway, but substantial evidence suggests that RecN is also involved in the RecBCD DSB repair pathway. Unlike other members of the RecF pathway, recN mutants are quite sensitive to ionizing radiation or mitomycin C, and the repair of multiple, site-specific DSBs does not occur in the absence of RecN (8,12,13). The recN gene is also required for the suppression of chromosomal rearrangements and deletions (12) during the repair of a single DSB. Given this wealth of genetic data, the RecN protein is clearly involve...

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“…Biophysical Journal 00(00) [1][2][3][4][5][6][7][8][9][10][11][12] These equations can be solved, producing from Eq. (7)…”

Section: Theoretical Modelmentioning

confidence: 99%

“…However, within a cell DNA molecules constantly experience attacks by various active chemical molecules, thermal collisions with other molecules and the effect of external radiation (2)(3)(4). This leads to frequent defects and even breaks in double-stranded DNA chains, which might be lethal for cells.…”

Section: Introductionmentioning

confidence: 99%

On the Mechanism of Homology Search by RecA Protein Filaments

Kochugaeva

Shvets

Kolomeisky

2017

Biophysical Journal

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Genetic stability is a key factor in maintaining, survival and reproduction of biological cells. It relies on many processes, but one of the most important is a homologous recombination, in which the repair of breaks in double-stranded DNA molecules is taking place with a help of several specific proteins. In bacteria this task is accomplished by RecA proteins that are active as nucleoprotein filaments formed on single-stranded segments of DNA. A critical step in the homologous recombination is a search for a corresponding homologous region on DNA, which is called a homology search. Recent single-molecule experiments clarified some aspects of this process, but its molecular mechanisms remain not well understood. We developed a quantitative theoretical approach to analyze the homology search. It is based on a discrete-state stochastic model that takes into account the most relevant physical-chemical processes in the system. Using a method of first-passage processes, a full dynamic description of the homology search is presented. It is found that the search dynamics depends on the degree of extension of DNA molecules and on the size of RecA nucleoprotein filaments, in agreement with experimental single-molecule measurements of DNA pairing by RecA proteins. Our theoretical calculations, supported by extensive Monte Carlo computer simulations, provide a molecular description of the mechanisms of the homology search.

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DNA replication meets genetic exchange: Chromosomal damage and its repair by homologous recombination

Cited by 198 publications

References 131 publications

Branched oligonucleotides induce in vivo gene conversion of a mutated EGFP reporter

Branched oligonucleotides induce in vivo gene conversion of a mutated EGFP reporter

RecN Is a Cohesin-like Protein That Stimulates Intermolecular DNA Interactions in Vitro

On the Mechanism of Homology Search by RecA Protein Filaments

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