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Reca Acts As a Switch to Regulate Polymerase Occupancy in a Moving Replication Fork

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Reca Acts As a Switch to Regulate Polymerase Occupancy in a Moving Replication Fork RecA acts as a switch to regulate polymerase occupancy in a moving replication fork Chiara Indiania,1, Meghna Patelb, Myron F. Goodmanb, and Mike E. O’Donnellc,1 aManhattan College, Riverdale, NY 10471; bDepartment of Biological Sciences, University of Southern California, Los Angeles, CA 90089; and cHoward Hughes Medical Institute, Rockefeller University, New York, NY 10065 Contributed by Mike O’Donnell, February 19, 2013 (sent for review February 6, 2013) This report discovers a role of Escherichia coli RecA, the cellular regulates DNA polymerase access to the replication fork. Sur- recombinase, in directing the action of several DNA polymerases prisingly, RecA strongly inhibits fork progression by Pol III repli- at the replication fork. Bulk chromosome replication is performed somes, yet RecA stimulates TLS Pol II and Pol IV replisomes. The by DNA polymerase (Pol) III. However, E. coli contains translesion mechanism that underlies the opposite effects of RecA on Pol III synthesis (TLS) Pols II, IV, and V that also function with the helicase, and the TLS Pol replisomes involves single-strand binding protein primase, and sliding clamp in the replisome. Surprisingly, we find (SSB). Although all of the polymerases function with SSB on the that RecA specifically activates replisomes that contain TLS Pols. In template strand, SSB inhibits TLS Pol function in the context of sharp contrast, RecA severely inhibits the Pol III replisome. Given a replisome, presumably acting in trans by binding lagging-strand the opposite effects of RecA on Pol III and TLS replisomes, we pro- ssDNA. RecA relieves the SSB induced repression of TLS Pol pose that RecA acts as a switch to regulate the occupancy of poly- replisomes and stimulates their action, while inhibiting the Pol III merases within a moving replisome. replisome. We propose that the opposite effects of RecA on Pol III and TLS Pol replisomes facilitate the switch of TLS Pols with DNA repair | lesion bypass | recombinase | translesion polymerase Pol III during the cellular response to DNA damage. Results ells contain several different translesion synthesis (TLS) RecA Inhibits the Pol III*-Replisome. The cellular replicase, Pol III*, DNA polymerases (Pols) that can synthesize DNA across C is composed of three Pol III cores attached to the three τ sub- BIOCHEMISTRY damaged nucleotides, but TLS Pols are typically low fidelity and units of the clamp loader [(Pol III) τ δδ′χψ] (18–20) (Fig. 1A). mutagenic (ref. 1 and references therein). In Escherichia coli, 3 3 One Pol III core functions on the leading strand, whereas the TLS Pol II and TLS Pol IV are present in normal growing cells other two Pol III cores extend multiple Okazaki fragments on along with the high-fidelity chromosomal replicase, Pol III. the lagging strand (20, 21). The τ subunits also connect to the Previous studies have shown that all three Pols function at rep- β hexameric DnaB helicase that encircles the lagging strand, lication forks with DnaB helicase, primase, the sliding clamp, forming a replisome that we refer to as the Pol III*-replisome in and the clamp loader (2). Bulk chromosome replication is per- this report (i.e., Pol III*-β-DnaB). Primase acts distributively and formed by Pol III, and the mechanism that regulates the access periodically targets the helicase for activity, ensuring that RNA of TLS Pols to the replisome is largely unexplored. E. coli primers are located near the replication fork (22). Heavy DNA damage in induces the SOS response, which To examine the effect of RecA on the Pol III*-replisome, we slows down chromosomal replication (3) and expresses over 40 used a 100-mer synthetic rolling circle DNA (Fig. 1A). The proteins that aid cell survival and enable genome replication to leading-strand template (inner circle) contains only dG, dC, dA, continue (4, 5). Induction of the SOS response requires formation enabling the leading strand (and not the lagging strand) to be of ssDNA by replication forks to which the cellular recombinase, labeled using [α-32P]dTTP. The DnaB helicase is first assembled RecA, binds. The binding of RecA to ssDNA facilitates RecA- onto the 5′ ssDNA tail in a 2-min preincubation, followed by mediated self-cleavage of the LexA repressor, thereby activating assembly of the Pol III*-β clamp in the absence of dTTP to the SOS response genes (6). Among these are TLS Pol II (polB) dinB < prevent forward progression during a further 4-min incubation. and TLS Pol IV ( ), which are rapidly ( 5 min) up-regulated DNA synthesis is initiated upon adding [α-32P]dTTP, the four during the SOS response (7–10). TLS Pol V (UmuD′2C) is induced ≥ ribonucleotide triphosphates (rNTPs), primase, and SSB. When late ( 45 min) and requires RecA bound to ssDNA (RecA*) for present, RecA is added 2 min before initiating DNA synthesis, synthetic activity (8, 11, 12). Pol IV and Pol V belong to the Y- unless indicated otherwise. Timed aliquots are withdrawn and family Pols (1), whereas Pol II, even though involved in TLS and DNA products are analyzed in an alkaline agarose gel. mutagenesis, is a B-family polymerase (13). The results of these assays show that RecA greatly inhibits During normal chromosome duplication, the intracellular levels leading-strand synthesis by the Pol III*-replisome (Fig. 1B). To fi of Pols II and IV are not suf cient to take over Pol III-based determine whether RecA inhibition occurs during elongation or replisomes (2). Upon DNA damage, the induced levels of TLS initiation, we tested the effect of adding RecA after DNA synthesis Pols take over the cellular replicase (2, 14, 15). Our previous has been initiated (Fig. 1C). The result shows that RecA also studies have shown that Pols II and IV replace Pol III within the inhibits a moving Pol III*-replisome. Thus, RecA up-regulation replisome without causing fork collapse, as they preserve the DNA- during the SOS response should inhibit fork progression by Pol bound helicase and sliding clamp to form TLS Pol replisomes (2). III*-β. Our earlier studies on the effect of RecA on Pol III*-β have Pol II and Pol IV replisomes progress at significantly slower rates than the intrinsic rate of DnaB helicase, and thus regulate the speed of helicase unwinding. Slower fork progression may give the Author contributions: C.I. and M.E.O. designed research; C.I. performed research; M.P. cell additional time to repair DNA lesions using normal repair and M.F.G. contributed new reagents/analytic tools; C.I. and M.E.O. analyzed data; and processes (e.g., nucleotide excision repair), thereby preventing C.I. and M.E.O. wrote the paper. direct encounters of the replication fork with DNA lesions. The authors declare no conflict of interest. It has been suggested that polymerase selection at the replica- Freely available online through the PNAS open access option. tion fork is mainly guided by mass action dictated by the con- 1To whom correspondence may be addressed. E-mail: [email protected] or centration of each polymerase and its affinity for the clamp (1, 14, [email protected]. fi 16, 17). However, the ndings of this report demonstrate that This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. RecA adds an additional level of control, acting as a switch that 1073/pnas.1303301110/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1303301110 PNAS Early Edition | 1of6 Downloaded by guest on October 2, 2021 destabilizes the Pol III*-replisome, facilitating its dissociation, consistent with our earlier in vitro observations that RecA dis- lodges Pol III* from a primed site (23). Another possibility is that RecA inhibits a component of Pol III*, either Pol III core, the clamp loader, or the τ subunit of the clamp loader. In Fig. 2, we examined the effect of RecA on Pol III core- replisomes lacking the τ subunit. Elimination of the τ subunit from the reaction is made possible by the fact that the dnaX gene encoding τ also encodes a smaller subunit, γ (28). The τ subunit can be replaced by γ within the clamp loader without effect on clamp- loading activity (29). However, unlike τ, the γ subunit cannot bind Pol III core and DnaB helicase. Without the connection between Pol III core and DnaB helicase, the Pol III core-replisome is much slower than the Pol III*-replisome (30). In addition, because the clamp loader contains three copies of either τ or γ (31), when γ replaces τ, leading- and lagging-strand polymerases are no longer connected together by the clamp loader. The effect of RecA on the Pol III core-replisome, assembled using Pol III core, β and the γ complex (Fig. 2A), shows that RecA no longer has a significant effect on the Pol III core-replisome (Fig. 2B). The absence of an effect by RecA indicates that RecA does not interfere with either Pol III core or the clamp loader. To test whether RecA interferes with the τ function, we added extra τ into Pol III*-replisome reactions containing RecA. Addition of excess τ only slightly inhibits the Pol III*-replisome (lanes 1 and 2). In contrast, excess τ partially restores activity of the Pol III*- replisome in the presence of RecA (Fig. 2C, lanes 3 and 4). We have not detected a physical interaction between τ and RecA, although such an interaction could be weak and hard to detect. The τ subunit is also known to bind ssDNA, and therefore RecA may compete with τ to bind ssDNA, decreasing the affinity of Pol III* to DNA and ejecting Pol III* from the fork. Pol III*-replisomes and Pol III core-replisomes also differ by the fact that leading- and lagging- strand synthesis are performed simultaneously by the Pol III*- replisome, but are physically uncoupled in replisomes containing Pol III core (i.e., τ is needed to connect Pol III cores together).
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