Double-strand break repair in bacteriophage T4: Coordination of DNA ends and effects of mutations in recombinational genes

Shcherbakov, Victor P.; Plugina, Lidiya; Shcherbakova, Tamara; Sizova, Svetlana; Kudryashova, Elena

doi:10.1016/j.dnarep.2006.03.007

Cited by 12 publications

(15 citation statements)

References 55 publications

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“…This could reflect UvsXYW-independent recombination reactions (perhaps single-strand annealing) or could reflect some essential role for the MR complex outside of the RDR reaction (see Discussion). Consistent with results mentioned above with the eukaryotic protein, genetic studies support a role for the T4 MR complex in end coordination during DSB repair (Shcherbakov et al 2006b; also see below).…”

supporting

confidence: 70%

Coordination and Processing of DNA Ends During Double-Strand Break Repair: The Role of the Bacteriophage T4 Mre11/Rad50 (MR) Complex

et al. 2013

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The in vivo functions of the bacteriophage T4 Mre11/Rad50 (MR) complex (gp46/47) in double-strand-end processing, double-strand break repair, and recombination-dependent replication were investigated. The complex is essential for T4 growth, but we wanted to investigate the in vivo function during productive infections. We therefore generated a suppressed triple amber mutant in the Rad50 subunit to substantially reduce the level of complex and thereby reduce phage growth. Growth-limiting amounts of the complex caused a concordant decrease in phage genomic recombination-dependent replication. However, the efficiencies of doublestrand break repair and of plasmid-based recombination-dependent replication remained relatively normal. Genetic analyses of linked markers indicated that double-strand ends were less protected from nuclease erosion in the depleted infection and also that end coordination during repair was compromised. We discuss models for why phage genomic recombination-dependent replication is more dependent on Mre11/Rad50 levels when compared to plasmid recombination-dependent replication. We also tested the importance of the conserved histidine residue in nuclease motif I of the T4 Mre11 protein. Substitution with multiple different amino acids (including serine) failed to support phage growth, completely blocked plasmid recombination-dependent replication, and led to the stabilization of double-strand ends. We also constructed and expressed an Mre11 mutant protein with the conserved histidine changed to serine. The mutant protein was found to be completely defective for nuclease activities, but retained the ability to bind the Rad50 subunit and double-stranded DNA. These results indicate that the nuclease activity of Mre11 is critical for phage growth and recombination-dependent replication during T4 infections.

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confidence: 70%

Coordination and Processing of DNA Ends During Double-Strand Break Repair: The Role of the Bacteriophage T4 Mre11/Rad50 (MR) Complex

et al. 2013

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“…RDR requires coordination of the DNA ends to ensure that reciprocal and symmetric events occur, thus replicating the complete genome (Stohr and Kreuzer, 2002;Shcherbakov et al, 2006). This process is not disrupted by mutations in MSH1 or RECA3, although it may be disrupted by mutations in the other RecA homologs, which would explain their lethality.…”

Section: The Sss Process Appears To Be Associated With Nuclear Regulamentioning

confidence: 99%

“…It could be degraded, undergo NHEJ, or invade another DNA molecule (Stohr and Kreuzer, 2002;Shcherbakov et al, 2006). If it invades the asymmetric recombination product and initiates replication, regeneration of the parental molecule would occur.…”

Section: The Sss Process Appears To Be Associated With Nuclear Regulamentioning

confidence: 99%

Plant Mitochondrial Recombination Surveillance Requires Unusual RecA and MutS Homologs

et al. 2007

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For >20 years, the enigmatic behavior of plant mitochondrial genomes has been well described but not well understood. Chimeric genes appear, and occasionally are differentially replicated or expressed, with significant effects on plant phenotype, most notably on male fertility, yet the mechanisms of DNA replication, chimera formation, and recombination have remained elusive. Using mutations in two important genes of mitochondrial DNA metabolism, we have observed reproducible asymmetric recombination events occurring at specific locations in the mitochondrial genome. Based on these experiments and existing models of double-strand break repair, we propose a model for plant mitochondrial DNA replication, chimeric gene formation, and the illegitimate recombination events that lead to stoichiometric changes. We also address the physiological and developmental effects of aberrant events in mitochondrial genome maintenance, showing that mitochondrial genome rearrangements, when controlled, influence plant reproduction, but when uncontrolled, lead to aberrant growth phenotypes and dramatic reduction of the cell cycle.

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“…The splice/patch coupling (SPC) pathway, substantiated earlier for the general genetic recombination and recombination-dependent replication (RDR) in bacteriophage T4 (Shcherbakov et al 1992), and corroborated also for the DSB-promoted recombination (Shcherbakov et al 2002(Shcherbakov et al , 2006, is depicted in Figure 1. The scheme illustrates interaction of two parental DNAs as in a cross i 3 ets1.…”

mentioning

confidence: 76%

“…The fc-SPC implies only repair DNA synthesis and does not lead to chromosome replication. Both variants of the SPC pathway seem to operate with a certain probability during DSB repair (Shcherbakov et al 2006). They give somewhat different predictions for the expected rII 1 recombinant frequencies.…”

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confidence: 97%

Double-Strand Break Repair in Bacteriophage T4: Recombination Effects of 3′–5′ Exonuclease Mutations

et al. 2006

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The role of 39-59 exonucleases in double-strand break (DSB)-promoted recombination was studied in crosses of bacteriophage T4, in which DSBs were induced site specifically within the rIIB gene by SegC endonuclease in the DNA of only one of the parents. Frequency of rII 1 recombinants was measured in two-factor crosses of the type i 3 ets1, where ets1 designates an insertion in the rIIB gene carrying the cleavage site for SegC and i's are rIIB or rIIA point mutations located at various distances (12-2040 bp) from the ets1 site. The frequency/distance relationship was obtained in crosses of the wild-type phage and dexA1 (deficiency in deoxyribonuclease A), D219A (deficiency in the proofreading exonuclease of DNA polymerase), and tsL42 (antimutator allele of DNA polymerase) mutants. In all the mutants, recombinant frequency in crosses with the i-markers located at 12 and 33 bp from ets1 was significantly enhanced, implying better preservation of 39-terminal sequences at the ends of the broken DNA. The effects of dexA1 and D219A were additive, suggesting an independent action of the corresponding nucleases in the DSB repair pathway. The recombination enhancement in the dexA1 mutant was limited to short distances (,100 bp from ets1), whereas in the D219A mutant a significant enhancement was seen at all the tested distances. From the character of the frequency/distance relationship, it is inferred that the synthesisdependent strand-annealing pathway may operate in the D219A mutant. The recombination-enhancing effect of the tsL42 mutation could be explained by the hypothesis that the antimutator 43Exo removes a shorter stretch of paired nucleotides than the wild-type enzyme does during hydrolysis of the unpaired terminus in the D-loop intermediate. The role of the proofreading exonuclease in the formation of a robust replicative fork is discussed. S HCHERBAKOV et al. (2002) developed a modelsystem for studying double-strand break (DSB) repair based on the ets1 segCD strain of bacteriophage T4. A 66-bp fragment of phage T2L containing the cleavage site for SegC endonuclease (ets1) was inserted into the proximal part of the rIIB gene in a T4 segCD strain. In crosses of the ets1 segCD with a segC 1 partner, SegC endonuclease makes a DSB in the middle of the ets1 insertion, thus promoting recombination on both sides of ets1. This focused recombination is an effective tool for studying genetic recombination and DSB repair in vivo.The splice/patch coupling (SPC) pathway, substantiated earlier for the general genetic recombination and recombination-dependent replication (RDR) in bacteriophage T4 (Shcherbakov et al. 1992), and corroborated also for the DSB-promoted recombination (Shcherbakov et al.

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Double-strand break repair in bacteriophage T4: Coordination of DNA ends and effects of mutations in recombinational genes

Cited by 12 publications

References 55 publications

Coordination and Processing of DNA Ends During Double-Strand Break Repair: The Role of the Bacteriophage T4 Mre11/Rad50 (MR) Complex

Coordination and Processing of DNA Ends During Double-Strand Break Repair: The Role of the Bacteriophage T4 Mre11/Rad50 (MR) Complex

Plant Mitochondrial Recombination Surveillance Requires Unusual RecA and MutS Homologs

Double-Strand Break Repair in Bacteriophage T4: Recombination Effects of 3′–5′ Exonuclease Mutations

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