Proc NatL Acad. Sd. USA Vol. 78, No. 1, pp. 69-73. January 1981 Biochemistry Unique primed start of phage 4x174 DNA replication and mobility of the primosome in a direction opposite chain synthesis (origin of complementary strand replication/protein n'/mobile replication promotor/antielongation direction/DNA-dependent ATPase) KEN-ICHI AMI* AND ARTHUR KORNBERG Department of Biochemistry. Stanford University School of Medicine, Stanford, California 94305 Contributed by Arthur Kornberg, Septemberl. 1980 ABSTRACT ent of the 4x174 viral circle sus- tains the primed start of compEentary DNA strand synthesis in oitro, even though the intact circlepermits primed starts at many sites. The 3Wnucleotide fragment rom restriction nuclease di es tion contains the recognition site for protein n', a DNA-depentfen; ATPase essential for priming 4x174 DNA replication. This n' rec- ognition site contains within it a 44-nucleotide se uence with a po- tential hairpin structure and maybe regarded as ftre startin signal for replication [Shlomai, J. & Kornberg, A. (198O)Proc Natf Acod Sci USA 77, 799-803]. After initiation on the 3' side of this se- quence, the priming system (primosome) repeatedly generates primers by moving processively on the DNA template in a direc- tion opposite to chain elongation. This primosome mobility is an attractive model for the discontinuous phase of Escherichia coli chromosome replication, in which processive primosome move- ment with the replicating fork is proposed for repeated initiations of nascent replication fragments. A specific fra Conversion of single-stranded DNA (ssDNA) of phage 4x174 (4X) to duplex replicative form (RF) is a model system (1-3) for the discontinuous phase of Escherichia coli chromosomal repli- cation in which the nascent replication (Okazald) bagments are initiated. In this conversion, 4X DNA coated by ssDNA-bind- ing protein (SSB) must first be activated in a prepriming stage for subsequent priming by primase (2, 4-6). In this prepriming reaction, E. coli proteins n, n', n", i, dnaC, and dmB interact to form a prepriming replication intermediate (4, 5, 7). Unlike phages M13 (8,9) and G4 (10-12), which possess unique origins for priming complementary strand replication, 4X permits mul- tiple starts in DNA replication, as indicated by both in oiuo (12) and in oitro studies (5, 7). However, the strict specificity of the prepriming system for 4X DNA (7, 13) and the specific recog- nition by protein n' of a 55-nucleotide sequence in c$X DNA, located in the same intergenic region as the G4 origin (14), strongly suggest a unique origin for 4X complementary strand replication. This present work shows that complementary strand replica- tion is in fact initiated at or near the protein n' recognition locus by a multiprotein-DNA complex (a mobile replication promoter or "primosome"), which then migrates with a unique polarity on the ssDNA template in a direction opposite to primer and DNA chain synthesis. Subsequent reports will describe participation of ATP in the processivity of primosome movement and conser- vation of the primosome in successive stages of @X DNA repli- cation. These studies ofprimosome structure and function have implications for events taking place at the E. coli chromosome replication fork. MATERIALS AND METHODS Nucleic Acids and Enzymes. DNAs, E. coli replication pro- teins, and other materials were as described (13-16). Restriction The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "duertipe- ment" in accordance with 18 U. S. C. 11734 solely to indicate this fact. endonuclease fragments of ssDNA (17, 18) for use as templates for DNA synthesis were prepared by digestion of 4X or G4 DNA (30 pg) at 37°C for 15 hr with Hue 111 (400 units) or Hha I endonuclease (320 units) in 400 pI of 50 mM Tris-HCI (pH 7.5)/ 5 mM MgClJ0.5 mM dithiothreitol. Digestion products were precipitated with ethanol from phenol-treated reaction mix- tures and dissolved in 50 mM Tris-HC1 (PH 7.5)/1 mM EDTA. Buffer A was 100 mM Tris-HCI (PH 7.5)/20% sucrose/40 mM dithiothreito1/200 pg of bovine serum albumin per ml. DNA Replication Assay. Components were added in order at 0°C and incubated 20 min at 30°C: 5 pI of buffer A, 1.2 nmol each of [3H] or [cK-~'P]~CTP, dGTP, dATP, and dTTP (each at 2000 dpm/pmol), 2.5 nmol each of GTP, CTP, and UTP, 20 nmol of ATP, 0.2 pmol of MgCl,, 450 pmol (as nucleotide) of 4X ssDNA or its digestion products, 0.25 pg of rifampicin, SSB as indicated, 0.2 pg of DNA polymerase 111 holoenzyme, 0.4 pg of dmB protein, 0.1 pg each of dnaC, i, and n' proteins, 0.14 pg of protein mixture n + n", 0.1 pg of primase, and water to 25 pl. With G4 DNA or its digests as templates, only SSB, DNA polymerase 111 holoenzyme, and primase were included. Other Methods. Agarose gel electrophoresis of DNA was as described (16, 19). The relative amount of 32P radioactivity in each band was determined by densitometric tracing of the auto- radiogram with a Quick Scan Jr. TLC, Helena Laboratories (Beaumont, TX). Sizes of DNA products were determined after heat denaturation in 98% (wt/vol) formamide by electrophore- sis in a 7 M urea/2.5-7.5% gradient polyacrylamide gel (5,20). Transfer of DNA to diazobenzyloxymethyl (DBM) papert and DNA hybridizations were as described (21.22). RESULTS Unique primed start of DNA replication Specific DNA Synthesis on a C4 DNA Fragment. Whether a unique primed start of DNA replication can be sustained by a fragment of a phage DNA circle was first determined with G4 DNA. A Hha I endonuclease digest (15 fragments) of G4 DNA (23) supported DNA synthesis with SSB, primase, and DNA polymerase 111 holoenzyme at 18% the level of untreated G4 DNA (Table 1). Omission of primase abolished almost 80% of this activity. Agarose gel electrophoresis of the G4 DNA prod- ucts showed that more than 90% ofthe DNA was synthesized on the 1494-nucleotide Hha I fragment 1, which contains the origin ~ Abbreviations: +X, phage 4x174; ssDNA, single-stranded DNA; RF, double-stranded DNA in the circular replicative form; SSB, ssDNA- binding protein; DBM, diazobenzyloxymethyl; p[NH]ppA, J'denyl- yl imidodiphosphate. *Present address: Department of Chemistry, The Institute of Medical Science, The University of Tokyo, 4-61. Shirokanedai. Minato-ku, Tokyo 108, Japan. t In some experiments, DNA fragments were transferred to aminothio- phenol paper, a procedure suggested by Brian Seed of the California Institute of Technology. 69 70 Biochemistry: Arai and Kornberg Proc. NatL Acad. Sci. USA 78 (1981) Table 1. Template activity ofHae III and Hha I endonuclease digests of phage DNA DNA synthesis, Riming pmol Nuclease treatment oftemplate wmponent(s) G4 &X None Hae III Hh I + 290 360 - 8 11 + 4 39 2 18 + 51 18 12 5 - - DNA synthesis was with 1.0 pg of SSB. The priming component for the G4 templates was only primaee; the priming wmponents for &X in- cluded the prepriming proteins n, n', n", i, dnaB, and dnaC, as well as primaee. of G4 complementary strand replication (10, 23) (Fig. 1). The extent of synthesis was nearly what was expected from the loca- tion of the origin within fragment l and its relative size. No DNA synthesis was detected with a Hue 111 endonuclease digest (14 fragments). Although the 442-nucleotide fragment Z5a contains the G4 complementary strand origin, the cleavage site is at the stem of the "downstream" hairpin located about 60 bases downstream from the start of the primer and presum- ably required for recognition by primase (24). These results in- dicate that for primase the circular form of DNA is not essential and that primase can recognize the specific signal for the com- plementary strand origin of G4 DNA even in a small DNA fragment. DNA Synthesis on a Unique Fragment of q5X DNA Requir- ing the Prepriming Proteins. DNA synthesis with an unfrac- tionated 4X DNA Hoe 111 digest (25) was 11% that with intact +X viral circle (Table 1). Omission of prepriming proteins n, n', n", i, and dnuC abolished only halfthe activity, suggesting some nonspecific initiation on DNA fragments. The effects of SSB on specific initiation dependent on prepriming proteins, and on i1h.b I c_: !?IO. 1. Autoradiogram of DNA prcducta synthesized on phage DNA Hae JII or Hha I endonuclease fragmenta. DNA synthesis was with saDNA or ita Hue III or Hha I digest: G4 with 1.5 pg of SSB, &X with 4 lrg of SSB. The DNA products were separated by electrophoreeis in a 1.5% agarose gel and detected with ethidium bromide (arrows) and autoradiography. SSB, M? FIG. 2. Effecte of SSB on specific and nonspecific DNA synthesis with +X DNA (A) and ita Hae UI endonuclease fragments (B1 as tem- plates. Reaction mixtures included only dnaB protein, primase, and DNA polymeraae III holoenzyme (o), or also prepriming proteins n, n' , n", i, dnaC. and dnaB (0). nonspecific initiation obtained with only dnaB protein and pri- mase (13), were examined with intact 4X circular DNA and its Hoe 111 fragments. Nonspecific initiation on the intact circle was inhibited almost completely by SSB (Fig. M), whereas that on the fragments was more resistant to SSB; an 80% inhibition re- quired a 4-fold excess of SSB beyond that needed to coat the ssDNA (26) (Fig. 28). At this high level of SSB, 85% of the DNA synthesis was dependent on prepriming proteins; the nonspe- cific DNA synthesis required only DNA polymerase 111 holoen- zyme (data not shown). Of the DNA produced with only dnaB protein, primase, DNA polymerase 111 holoenzyme, and 1.5 pg of SSB, 19%, %%, and 53% was synthesized on the Z1,23, and 24 fragments, respectively (Fig. 3, trace a). When prepriming proteins n, n', n", i, and dnaC were included, these ratios changed to 53%. 338, and 14% (Fig. 3, trace b), suggesting that prepriming pro- teins stimulate specific initiation on the Z1 fragment and sup- press nonspecific initiation on the Z4 fragment. With a 4-fold excess of SSB (3.6 pg) over that needed to coat the ssDNA (26). DNA synthesis on the 23 and ZA fragments was preferentially inhibited; 822, 12%, and 6% of the DNA was synthesized on the Z1, 23, and Z4 fragments, respectively (Fig. 1 and Fig. 3, trace c). Other Hue 111 fragments were completely inert. These results demonstrate that SSB inhibits nonspecific DNA synthe- sis and that the 1353-nucleotide Z1 fragment is specifically ac- tivated as a template for DNA replication by prepriming pro- teins and primase. 24 Y "i "1" ad bL L Electrophoresis FIG. 3. ['%']DNA products synthesized on Hoe III endonuclease fragmenta of &X DNA. DNA synthesis wan with 450 pmol (as nuclm tide) of Hae III digests of &X ssDNA, including in trace a only dnaB protein, pnmaae, DNA polymeraae XII holoenzyme, and 1.5 pg of SSB hce b, prepriming proteins n, n', n", i, and dnaC, as well as the pro- teins in trace a; and trace c, the proteins in trace b except that 4 pg of SSB wan used. DNA producte were fractionated by electrophoresis in 1.5% agarose gel and quantitated by densitometric tracings of '9 au- toradiograms. Arrows indicate the Hoe III fragments. Biochemistry: Arai and Kornberg Proc. Natl Acad. Sci. USA 78 (1981) 71 . 1 r' 23 > 24. These results indicate that the primosome migrates in the direction Z1+ 22 + 23 + ZA, consistent with the prediction of the antielongation direction model. DISCUSSION The prepriming system reconstituted in oitro from six E. coli proteins is highly.specific for 4X DNA coated with SSB (13). This specificity apparently derives from the capacity of protein n' to recognize and bind a specific intergenic sequence. This initiating event in complementary strand synthesis is obscured by rapid movement of the priming system (primosome) around the circular template, leading to the apparently random prim- ing and DNA syntheses observed in uioo and in oitro. In the Biochemistry: Arai and Kornberg Proc. Natl. Acad. Sci. USA 78 (1981) 73 present studies, primosome movement was restrained by using DNA hgments generated by endonucleases Hue I11 and Hha I (17, 18). Only hgments containing the protein n' recognition site were effective in sustaining the prepriming, priming, and DNA synthetic actions. Elevated levels of SSB were needed to suppress nonspecific priming and replication. In view of the complexity of prepriming, it is remarkable that the 300-nucleotide Hha I fragment 6 suffices for the specificity for chain initiation on 4X DNA. The DNA product size, 250 res- idues, suggests that primers are made at or near the haupin within the 55-nucleotide protein n' recognition locus where, presumably, primosome assembly takes place. The effect of protein n' binding and primosome assembly at this site needs to be clarified. Because p[NH]ppA sufTices far the formation of a prepriming replication intermediate (unpublished result), hy- drolysis of ATP and movement ofprotein n' or dnaB protein are not prerequisites for initial primosome assembly. The remark- able feature of the unique origin for 4X complementary strand synthesis is that this site is not necessarily defined as the site where a unique primer is made. Rather it may be defined as the site for assembly of the primosome, which then may migrate processively along the viral circle. As will be described else- where, the energy of ATP and dATP hydrolysis utilized by pro- tein n' is essential to promote priming at many regions. Presum- ably protein n' not only recognizes the origin of complementary strand replication but also drives the primosome along the DNA strand. In the present study, polarity of primosome migration was shown to be uniquely in the ontielongation, the 5'+3',direc- tion of the template (Fig. 5). This is consistent with the pro- ped mobility of the primosome on the lagging strand at the replication fork (3,s). movement of the replication fork and pri- mosome taking place in the same direction. Thus Far, the polar- ity of primosome migration has been determined only when coupled to priming and DNA elongation. Approximately one primer is made per circle despite a capacity to synthesize mul- tiple primers when uncoupled from DNA elongation (ref. 5; un- published results). This indicates that the primosome can mi- grate in the 5'+3' direction before priming. The random distribution of primers on 4X DNA when preincubated with ATP to form the prepriming replication intermediate suggests that the.primosome moves along the DNA template even with- out primase action. Whether this migration of a primosome lacking primase is unidirectional with a 5'43' polarity remains to be clarified. This work W~LE supported in part by grants from the National Institutes of Health and the National Science Foundation. K.A. is a Fellow of the American Cancer Society. 1. 2. 3. 4. 5. 6. 7. a. Q. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. 26. 27. 28. Schekman, R., Weiner, A. & Kornberg, A. (1974) Science 186. 987-993. Wickner, S. & Hunvik, J. (1974) Proc. Natl. Acad. Sci. USA 71, 4120-4124. 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