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(NAS Colloquium) Links Between Recombination and Replication: Vital Roles of Recombination (2002)
Proceedings of the National Academy of Sciences (PNAS)

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246
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Colloquium on Links Between Recombination and Replication: Vital Roles of Recombination

radiation, whereas those in S phase responded efficiently. A single fraction (no. 7) contained predominantly G2 cells and this fraction showed less focus induction than did the previous fraction that contained mostly S-phase cells at the time of radiation treatment. However, this result could be misleading because the number of cells recovered in fraction no. 7 was quite low, reducing the reliability of FACS analysis. Furthermore, in other experiments, G2-enriched fractions showed efficient induction of Rad51 foci (data not shown). In contrast to the variable result with G2-enriched fractions, we consistently see failure of G1 cells to induce Rad51 foci and efficient induction of foci in S-phase cells. Induction of recombinational repair capability in S phase makes biological sense, in that most of the spontaneous DNA damage repaired by the recombinational mechanism occurs as a result of detects in replication (see ref. 103 and references therein).

Although changes in Rad51 expression level alone could account for the failure of G1 (and possibly G2) cells to form Rad51 foci in response to radiation, other regulatory processes may influence this response as well. Several lines of evidence from mammalian cells and yeast indicate that RPA, Rad51, and Rad55 are all phosphorylated in response to radiation (104108). Phosophorylation of these proteins is mediated by members of the ATM family of protein kinases in mammals and yeast. The activity of these kinases is induced in response to damage. ATM-dependent phosphorylation of Rad51 is mediated indirectly through ATM-dependent activation of the nonreceptor tyrosine kinase c-Abl (107, 108). One study found that phosphorylation of Rad51 by c-Abl increased Rad51-Rad52 interaction (108), a change that would be expected to enhance assembly of Rad51 in response to damage. However, another study found that phosphorylated Rad51 had reduced ability to bind ssDNA and was inactive in strand exchange reactions (107). Perhaps two pools of Rad51 are required for an efficient repair after damage, a phosphorylated pool to promote filament initiation via Rad52 interaction and an unphosphorylated pool critical for filament elongation and strand exchange. Another possibility is that phosphorylation of Rad51 contributes to cell-cycle regulation of Rad51 activity. Further studies are required to determine the role of posttranslational modification in assembly of recombination complexes in vivo and in vitro.

Future Directions for the Study of Recombinase Assembly. Substantial progress has been made in the last few years on the mechanisms that promote assembly of RecA-like recombinases. Important questions remain to be addressed. What are the structural intermediates involved in recombinase assembly? How is mediator activity regulated to ensure that recombinase assembles only at sites of DNA damage and not on the tracts of ssDNA that form as normal intermediates in DNA replication? Does mediator binding at DNA ends play an important part in recombinase assembly? Are the requirements for assembly at ends different from the requirements for assembly at daughter strand gaps? Why are mediator requirements stricter in meiosis than in mitosis? Does down-regulation of Rad51 protein alone account for the inability of G1 cells to form Rad51 foci in response to damage, or are other regulatory mechanisms in place? What role does damage-dependent phosphorylation play in recombinase assembly?

Bacteriophages have often provided paradigms of broad relevance to biological systems. This is certainly true in the case of recombinase assembly where the lessons learned from phage have guided experiments in bacteria, yeast, and higher eukaryotes. On the other hand, demonstration of different mediator requirements in mitosis and meiosis contributes to evidence indicating that some of the mechanisms regulating assembly of recombination complexes are unique to eukaryotes.

We thank Steve Kowalczykowski, Tim Lohman, Shunichi Takeda, Scott Morrical, John Petrini, and Akira Shinohara for helpful conversations. We also thank Jeff Murley and David Grdina for technical advice on centrifugal elutriation. This work was supported by a National Institute of General Medical Sciences Grant GM50936 awarded to D.K.B.

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Front Matter (R1-R3)
Links between recombination and replication: Vital roles of recombination (8172-8172)
Historical overview: Searching for replication help in all of the rec places (8173-8180)
Rescue of arrested replication forks by homologous recombination (8181-8188)
Circles: The replication-recombination-chromosome segregation connection (8189-8195)
Participation of recombination proteins in rescue of arrested replication forks in UV-irradiated Escherichia coli need not involve recombination (8196-8202)
Effects of mutations involving cell division, recombination, and chromosome dimer resolution on a priA2::kan mutant (8203-8210)
RecA protein promotes the regression of stalled replication forks in vitro (8211-8218)
Topological challenges to DNA replication: Conformations at the fork (8219-8226)
Rescue of stalled replication forks by RecG: Simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation (8227-8234)
Formation of Holliday junctions by regression of nascent DNA in intermediates containing stalled replication forks: RecG stimulates regression even when the DNA is negatively supercoiled (8235-8240)
Single-strand interruptions in replicating chromosomes cause double-strand breaks (8241-8246)
Handoff from recombinase to replisome: Insights from transportation (8247-8254)
Break-induced replication: A review and an example in budding yeast (8255-8262)
Links between replication and recombination in Saccharomyces cerevisiae: A hypersensitive requirement for homologous recombination in the absence of Rad27 activity (8263-8269)
Evidence that replication fork components catalyze establishment of cohesion between sister chromatids (8270-8275)
Rad52 forms DNA repair and recombination centers during S phase (8276-8282)
A yeast gene, MGS1, encoding a DNA-dependent AAA+ ATPase is required to maintain genome stability (8283-8289)
The tight linkage between DNA replication and double-strand break repair in bacteriophage T4 (8290-8297)
Mediator proteins orchestrate enzyme-ssDNA assembly during T4 recombination-dependent DNA replication and repair (8298-8305)
Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer (8306-8311)
Bacteriophage T4 gene 41 helicase and gene 59 helicase-loading protein: A versatile couple with roles in replication and recombination (8312-8318)
Instability of repetitive DNA sequences: The role of replication in multiple mechanisms (8319-8325)
Repeat expansion by homologous recombination in the mouse germ line at palindromic sequences (8326-8333)
Stationary-phase mutation in the bacterial chromosome: Recombination protein and DNA polymerase IV dependence (8334-8341)
Managing DNA polymerases: Coordinating DNA replication, DNA repair, and DNA recombination (8342-8349)
Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli (8350-8354)
Accuracy of lesion bypass by yeast and human DNA polymerase n (8355-8360)
ATP bound to the orgin recognition complex is important for preRC formation (8361-8367)
Creating a dynamic picture of the sliding clamp during T4 DNA polymerases holoenzyme assembly by using fluorescence resonance energy transfer (8368-8375)
Interaction of the ß sliding clamp with MutS, ligase, and DNA polymerase I (8376-8380)
Defining the roles of individual residues in the single-stranded DNA binding site of PcrA helicase (8381-8387)
Homologous DNA recombination in vertebrate cells (8388-8394)
Meiotic recombination and chromosome segregation in Schizosaccharomyces pombe (8395-8402)
Manipulating the mammalian genome by homologous recombination (8403-8410)
Assembly of RecA-like recombinases: Distinct roles for mediator proteins in mitosis and meiosis (8411-8418)
Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA (8419-8424)
Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: A possible advantage of DNA over RNA as genomic material (8425-8432)
The synaptic activity of HsDmc1, a human reccombination protein specific to meiosis (8433-8439)
Complex formation by the human RAD51C and XRCC3 recombination repair proteins (8440-8446)
Rad54 protein stimulates the postsynaptic phase of Rad51 protein-mediated DNA strand exchange (8447-8453)
The architecture of the human Rad54-DNA complex provides evidence for protein translocation along DNA (8454-8460)
DNA replication meets genetic exchange: Chromosomal damage and its repair by homologous recombination (8461-8468)
Colloquium Program (8469-8471)