A MINUTE CIRCULAR DNA FROM ESCHERICHIA COLI 15* By Nicuotas R. CozzarE.ui,t Reeis B. Ketiy,t anp ARTHUR KORNBERG DEPARTMENT OF BIOCHEMISTRY, STANFORD UNIVERSITY SCHOOL OF MEDICINE, PALO ALTO, CALIFORNIA Communicated May 10, 1968 In the course of preparing the intracellular replicative form of phage ¢X174 DNA (RFI), 2 we discovered an even smaller duplex circular DNA. This new DNA, synthesized by uninfected as well as infected cells of Escherichia coli, may be either an episome or a plasmid.’ For lack of evidence indicating its integra- tion into the chromosome, we regard it provisionally asa plasmid. In this report we describe some of the physical properties of this DNA and its distribution among strains of &. coli. The function of this plasmid remains unknown. Experimental Procedure.—Materials: Sources were as follows: CsCl (optical grade) was obtained from Harshaw; Brij 58, a nonionic detergent, from Atlas Chemical; Sepha- rose 4B from Pharmacia; egg-white lysozyme from Calbiochem; pancreatic DNase from Worthington; H*-deoxythymidine from New England Nuclear Corp.; and ethidium bromide, a gift from Boots Pure Drug Co., Nottingham, England. Methods: Cells were labeled with H*-thymidine (1-2 * 10’ cpm/yzmole) by growth in Fraser and Jerrel’s glycerol-casamino acids medium;' cells labeled with P#? (5-9 x 108 cpm/pmole) were grown in a medium described by Hershey,® supplemented with a mix- ture of the 20 natural amino acids. Cultures were harvested in the logarithmic phase at an Aso of 1.5-2.0. Cytoplasmic DNA was released from cells by the following modification® of the Godson and Sinsheimer lysis procedure.’ To about 5 X 10” cells suspended in 1 ml of 25% sucrose, 0.05 M Tris HCl, pH 8.0, were added 0.2 ml of lysozyme (5 mg/ml in 0.25 M Tris HCl, pH 8.0) and 0.4 ml of 0.25 M Na,EDTA. Conversion to spheroplasts was essentially complete after a 10-min incubation at 25°. The spheroplasts were ruptured by a further 10-min incubation at 25° with Brij added to a final concentration of 0.5%. Cellular debris and 90-98% of the total DNA were removed by sedimentation at 60,000 X g for15 min. At this stage, extracts may be analyzed for plasmid DNA by sucrose gradient sedimentation. For the further purification of plasmid DNA, the supernatant fluid was extracted three times with redistilled phenol and the phenol removed by extraction with ethyl ether. The solution was concentrated to an Ass of 500 by rotary evaporation and then digested with pancreatic ribonuclease (0.3 ug/ml for 10 min at 37°) to the point where 10% of the RNA became acid-soluble. The RNA fragments were removed by filtration through a column of Sepharose 4B with a bed volume ten times that of the sample. The duplex covalently closed plasmid DNA was separated from circular duplexes bearing single- strand breaks and linear forms by banding in a solution of CsCl (p = 1.57 gm cm~*) and ethidium bromide (100 ug/ml) for 36 hr or more at 40,000 rpm and 5° in the 50 rotor of the Spinco model L ultracentrifuge.? The last step was repeated if the product was less than 90% pure as judged by sedimentation in alkali. Ethidium bromide was removed by extraction with an equal volume of isopropanol or by passage through a Dowex-50 column.’ The final material was dialyzed against 0.05 M potassium phosphate buffer, pH 7.2,and1 mM EDTA. The yield of plasmid DNA from a 20-liter culture harvested at an Ass of 1.5 was about 0.4 umole (expressed as nucleotide residues). Sucrose gradient sedimentation of DNA samples was carried out as previously de- scribed.* The buffer contained: for neutral low-salt sedimentation, 10 mM Tris HCl, pH 8.0, and 1 mM EDTA titrated to pH 8.0 with NaOH; for neutral high-salt sedimentation, 1 M NaCl in addition; and for alkaline high-salt-sedimentation, 0.8 M NaCl, 1 mM EDTA, and 0.3 44 NaOH. Analytical determinations of buoyant density were made in 992 VoL. 60, 1968 BIOCHEMISTRY: COZZARELLI ET AL. 993 CsCl solution (p = 1.70 gm cm) in the Spinco model E ultracentrifuge at 44,000 rpm. Kel-F centerpieces were employed in standard cells. Ultraviolet absorption photographs were taken at regular intervals and subsequently scanned with a Joyce-Loebl recording microdensitometer. DNA was viewed with a Siemens Elmiskop 1A electron microscope using the protein film technique of Kleinschmidt e? al. as modified by Inman e? al.!1_ The hypophase was water. Magnification was determined from a diffraction grating of known line spacing. Colicin 15 was assayed by the procedure of Mukai?? with Z. coli strain TAU™ as the indicator and the colicin-resistant strain THU" as a control. The dose of UV light used to induce colicin production was 900 ergs mm~?. Results —Duplez circular plasmid DNA: In cells of strain THU, infected with ¢X174, a form of DNA in addition to RFI of ¢X174 was discovered. This new DNA had a density in an ethidium bromide-CsCl gradient characteristic of closed circular duplex DNA and sedimented less rapidly than ¢X174 RFI. The ratios of sedimentation velocities in alkaline high-salt, neutral high-salt, and neutral low-salt sucrose gradients were 0.65, 0.76, and 0.71, respectively. DNA with these same sedimentation properties was also found in uninfected cells. Thus, this new DNA appears to be a plasmid form of host cell DNA. The ratio of the alkaline to neutral sedimentation rates for the plasmid DNA is several times that anticipated for a linear duplex" and is consistent with a closed circular duplex structure.'* This supposition was tested by the action of pancreatic DNase. Purified plasmid DNA, sedimented to equilibrium in a CsCl gradient in the presence of ethidium bromide, yielded over 90 per cent of the DNA at a density value characteristic of 6X174 RFI (Fig. 1A). When single-strand scis- sions were introduced with pancreatic DNase, the DNA shifted into the lighter peak occupied by an RFII marker (Figs. 1B, C). This effect of pancreatic DNase on the banding pattern strongly supports a closed circular duplex structure of the plasmid DNA.’ , Contour length: The circular form of the plasmid DNA was also revealed by electron microscopy with the Kleinschmidt protein film technique (Fig. 2). The contour length was found to be 0.96 » + 0.13 (sp) for the plasmid DNA and 2.26 » + 0.13 (sp) for 6X 174 RFTI included on the same grids. The two samples of DNA were mixed and spread together to provide an internal control for the variations in absolute length measured by electron microscopy.’” '* Based on a molecular weight of the ¢X174 RF of 3.4 X 106 daltons,'* that of the plasmid DNA is calculated to be 1.45 K 108. The molecular length distributions shown in Figure 3, as well as the standard deviations, show that the length variation is similar for both types of DNA and thus that the cytoplasmic DNA has a rather homogeneous size distribution. In a separate experiment in which no ¢X174 RFII standard was added, only small circles and no polymeric forms® ®. #1. % 22 were found among 93 molecules examined. Furthermore, when the cytoplasmic DNA was analyzed on an alka- line sucrose gradient, no peak of radioactivity (less than 0.3%) was detectable at the position anticipated for dimers. Buoyant density: The buoyant densities of plasmid and T7 DNA were com- pared with that of poly dAT (p = 1.678)?5 as a standard. The plasmid DNA (p = 1.710) was 0.001 gm cm~ lighter than the T7 DNA. Since T7 and E. colt 994 BIOCHEMISTRY: COZZARELLI ET AL. Proc. N. A. 8. 1000 r BDNose ¥ 7 | somyug/ml 4 on —2— 19 sf 20 Fig. 1.—The effect of pancreatic DNase . treatment on banding of plasmid DNA in a CsCl-ethidium bromide gradient. Samples were centrifuged in a 1.5-ml solution of CsCl (0.75 gm/ml), 5 mM EDTA, and ethidium bromide (100 ug/ml) at 45,000 rpm, 10°C, | for 48 hr in the SB405 rotor of the Inter- + national B60 ultracentrifuge. The arrows + indicate the position of a marker of ¢X174 4 RFIIDNA. The plasmid DNA was treated . with DNase at the indicated concentrations for 60 min at 37°. Hl 1 v 5 10 15 20 Fraction number DNA have equal densities,?* the calculated GC content?* of the plasmid DNA is comparable to that of Z. coli chromosomal DNA. The half-width of the plasmid DNA band was 0.005 gm cm~—, which is in the expected range for a DNA of its size,” indicating a lack of extensive density heterogeneity. Molecular weight: Since the relationship between sedimentation velocity and molecular weight for closed duplexes is complicated by the number of tertiary turns,'* the sedimentation velocities of the open or “nicked” form of the plasmid DNA and of ¢X174 RFII were compared. To ensure that the pancreatic DNase was introducing only single-chain and not double-chain scissions into the P?*- labeled plasmid DNA, conditions were chosen which supported the conversion of at least 90 per cent of H?-lableled ¢X174 RFI (in the same reaction tube) to the nicked circular RFII. The neutral and alkaline sedimentation velocities gave molecular weight values of 1.53-1.63 X 10° daltons (Table 1), in good agreement with the value of 1.45 X 10° obtained from the contour lengths. Tertiary structure: ‘To determine whether the closed molecules contain tertiary turns, the ratio of the neutral sedimentation rates of the closed and open forms of the plasmid DNA were compared with that for ¢X174 RF and with the published value for phage ADNA.™ The presence of tertiary turns in a DNA increases its sedimentation coefficient.'° For plasmid DNA, at both high and low ionic strengths, this ratio was greater than one, which indicates that the DNA contains tertiary turns under these conditions (Table 2). The increase in the ratio of sedimentation velocities at low ionic strength was marked for \DNA, insignifi- Vou. 60, 1968 BIOCHEMISTRY: COZZARELLI ET AL. 995 Fic. 2.—Electron micrograph of plasmid and ¢X174 RFIT DNA. The smaller circles are the plasmid INA, and the larger the viral RF. cant for the plasmid, and intermediate for ¢X174 RI, suggesting that this ionic strength dependence is a function of molecular weight. Number of plasmids per chromosome: This value was estimated from the frac- tion of the total DNA recovered as plasmid DNA in the supernatant after deter- gent lysis. Spheroplasts of strain THU, uniformly labeled with H*-thymidine, were lysed with Brij, and the amount of plasmid DNA in the supernatant fluid was measured by sedimentation in an alkaline sucrose gradient with a marker of purified P3-labeled plasmid DNA. Three such determinations gave percentage values for the plasmid DNA of 0.64, 0.77, and 0.80 of the total cellular DNA. Assuming a molecular weight of 2.8 X 10° for the resting &. coli chromosome,” and 1.5 X 10° for the plasmid DNA, there are, on the average, 12 to 15 copies of ‘ plasmid DNA per chromosome. Our estimate of the number of plasmids might be low because of breakage of DNA during handling, the possible natural occur- rence of open forms (analogous to ¢X174 RII), or incomplete extraction. The first two sources of error are probably not significant because single-stranded DNA of molecular weight 7 10° was not detectable by alkaline sucrose sedimentation. of DNA from Brij-lysed cells. To determine whether plasmid DNA was sedi- mented with the host DNA after Brij lysis, the yield with this technique was compared to that after Sarcosy! lysis** and phenol extraction of the total cellular DNA. Both extraction procedures gave yields which differed by less than 50 per cent. Occurrence of plasmids in various iv. colt strains: The studies deseribed up to this point were conducted with strain THU, a derivative of strain 15. Nine other strains of 1, colt were also tested for the presence of the plasmid DNA 996 BIOCHEMISTRY: COZZARELLI ET AL. Proc, N. ALS. oO: 8504 3 e 3% w 230 re : : : 2 Fig. 3.—Distribution of contour 5 20- lengths of plasmid DNA and - @X174 RFI. Linear or aggre- 10k gated molecules were not included in these measurements; the ma- jority of the forms were circular. Oo 04 08 12 16 20 24 28 Contour length, microns (Table 3). H®-thymidine-labeled cells were lvsed with Brij, and the supernatant fraction was analyzed on an alkaline sucrose gradient (and in several cases also on a neutral suerose gradient) with a marker of purified P-labeled cytoplasmic DNA from strain THU. All derivatives of strain 15 showed a similar peak of radioactivity coincident with the P?? marker. Figure 4A shows one such experi- ment. Also, the DNA from strain 15T—D3 was purified and its contour length determined. The length, 1.03 1 + 0.09 (sp), was the same within experimental error as that determined for the plasmid from strain THU. In contrast to these results with derivatives of strain 15, no cytoplasmic DNA (<0.02% of the total DNA or <0.4 plasmid per chromosome) was detected in the strain K12 and B derivatives. One such experiment is shown in Figure 4B. It is possible that plasmids are synthesized by these strains but that extrachromosomal DNA is degraded or is not released by our lysis procedure. This possibility appears un- likely for the IX12 strains, at least, since high yields of ¢X174 RII can be ob- tained from these strains by this procedure. It therefore appears that, among the strains examined, the plasmid DNA is specific to strain 15. Discussion.—All the derivatives of strain 15 studied possess the plasmid DNA Taste 1. Molecular weight of plasmid DNA. Buffers Neutral Neutral Alkaline high salt low salt high salt Relative sedimentation velocity of ¢X174 RFII to strain 15 plasmid DNA (open form) 1.32 1.29 1.35 Mol wt of plasmid DNA ( x 10~*) 1.43 1.68 1.61 The sedimentation buffers are described in Methods. The ratio of sedimentation velocities is the average of 2-4 determinations and the average error ix 1%. The molecular weights were calculated from the equation of Studier." TABLE 2. Effect of single-strand scissions on sedimentation velocity of circular DNA. Relative sedimentation velocities of closed vs. EB. coli Circular open forms plasmid oX174 RF DNA High salt buffer 1.24 1.25 1.32* Low salt. buffer 1.26 1.37 1.67* The sedimentation buffers are described in Methods. * From Bode and Kaiser. Vou. 60, 1968 BIOCHEMISTRY: COZZARELLI ET AL. 997 TaBLe 3. Occurrence of plasmid DNA among ten strains of F. colt. E. colt Colicin 15 UV-light Plasmid Strain subspecies Reference production sensitivity DNA THU 15 14 - Ss + TAU 15 13 + Ss + TAU-e 5 29 - 8 + TAU-bar 15 30 — R + 15T~- 15 31 + S + 15T-D3 15 32 + S + JGI51 15 33 ~ T + B3 B 34 _ R - HF4704 Kl12 3) - R - HF4733 Kl2 36 ~ R - All strains are thymidine auxotrophs; additional requirements are cited in the references. The lytic response to UV light was determined by irradiation of cells with 900 ergs mm ~ of UV light and subsequent turbidemetric monitoring of growth. For sensitive (S) strains, there was about a fivefold decrease in optical density several hours after irradiation; for the tolerant (7) strain there was only a slight drop in turbidity; resistant (#) strains continued to grow. Colicin assays were performed on chloroform-treated cultures 6-8 hr after UV irradiation, the time of maximal clearing for sensi- tive strains. Strains listed as not producing colicin failed to do so even after a tenfold concentration. Strains THU, HF4704, and HF4733 were obtained from R. L. Sinsheimer;® TAU and TAU-bar from P.C. Hanawalt;* TAU-e and 15T ~D3 from K. Matsubara;® 15T ~and JG 151 from A. Yudelevich;%4 und B3 from N. E. Melechen.** even though some of these mutants were isolated as long as 14 vears ago.?! Moreover, the only common parent of these strains is strain 15 itself which was first described in 1944.%7 °° This genetic stability suggests a mechanism for maintaining the plasmid in the population, perhaps an orderly segregation of plasmids to daughter cells. It is further possible that occasional cured strains are at a selective disadvantage or can be reinfected with the plasmid. The plasmid DNA level of 15 copies per chromosome is high, especially since it was found in exponentially growing cells and thus represents a steady-state value.** By contrast there is only about one Flac or FColVColBtrycys*! particle per chromosome. Multiple copies of a drug-resistance factor were found only after transfer from an £. coli donor to a Proteus mirabilis recipient.** Tf we assume that the many copies of plasmid DNA are genetically identical, a reason- able assumption in light of their uniform molecular weight and density homoge- neity, then it is puzzling why the cell maintains such extensive genetic redundancy. Still a further question is the mechanism whereby the cell maintains the number of copies of the chromosome and the plasmid at such markedly different levels. The ease of identification of the plasmid DNA may make it a favorable system for study of this mechanism of replicon” control. The failure to detect the plasmid in IX12 or B led us to look at the properties of strain 15 that are not shared by B and X12. Some derivatives of strain 14 pro- duce a particulate colicin (colicin 15) which is apparently a defective phage. *? It is not likely that the small plasmid DNA codes for the defective phage because the virus appears to be large and thus would be expected to have a much larger DNA. Also, four of the strains analyzed, THU, TAU-bar, TAU-e, and JG151, do not produce colicin 15 but nevertheless contain the plasmid DNA (Table 3). Strain TAU-c was obtained from TAU under curing conditions”? and specifically lost the ability to produce colicin while retaining its plasmid DNA. Strain JG151 has also lost two other unusual properties associated with strain 15: high sus- 998 BIOCHEMISTRY: COZZARELLI ET AL. Proc. N.A.S. 600r—y T 1 T T T T oT A. Strain JG151 B. Strain Bs 500 -1F- 4 e 4007 VW 180 2 ‘ g . E 500 ‘e i de {603 v $ qi ? z l I 4 200+ tf: I +40 ” $ i e t { 100F- \ st: | \ -120 p We vececeat! tetas f 4 *~ d4 ‘4 i ! | Meepebosssheogtenet tose 3 30 { 5 10 158 «620-2530 5 10 15 20 25 Fraction number Fic. 4.—Neutral high salt-sucrose sedimentation of H?-labeled DNA from strain JG151 (A) and strain B3 (B). P#?-labeled plasmid DNA from strain THU was included for reference. ceptibility to thymineless death,?? and the induction of a new methylase by UV irradiation.‘4 The induction of lysis by UV irradiation is still another property of some derivatives of strain 15 that also is not necessarily correlated with the pres- ence of the plasmid DNA (Table 3). Thus far we have been unable to ascribe any biological function to this DNA. The strain 15 plasmid DNA is the smallest monodisperse DNA species thus far described,’ and the smallest. microbial DNA of any kind.® One of its strands could code for a polypeptide of only 75,000 in molecular weight and thus could contain very few cistrons. Its small size, relative abundance, ease of separation from chromosomal DNA, and its location in E. colt make it a convenient source of material for the investigation of DNA structure, replication, and function. Summary.—Strains of Escherichia coli 15 contain a supertwisted, circular, plasmid DNA with a molecular weight of 1.5 million, the smallest known micro- bial DNA. There are about. 15 plasmids per chromosome in the strain 15 cells but none was detected in strains of FE. coli X12 or B. * This work was supported in part by research grants from the National Institutes of Health (USPHS) and the National Aeronautics and Space Administration, + National Science Foundation postdoctoral fellow. t Helen Hay Whitney postdoctoral fellow. 1 Abbreviations: RFI and RFII denote the covalently closed and open duplex replicative forms of @X174 DNA, respectively; EDTA, ethylenediaminetetraacetate; Tris HCI, tris (hydroxymethyl)aminomethane HCI; poly dAT, polydeoxyadenylate-deoxythymidylate. 2 Burton, A., and R. L. Sinsheimer, J. Mol. Biol., 14, 327 (1965). 3 Jacob, F., and E. L. Wollman, Seruality and the Genetics of Bacteria (New York: Academic Press, 1961). 4Fraser, D., and E. A. Jerrel, J. Biol. Chem., 205, 291 (1953). 5 Hershey, A. D., Virology, 1, 108 (1954). ®§ Komano, T., and R. L. Sinsheimer, Biochim. Biophys. Acta, 155, 295 (1968). 7 Godson, G. N., and R. L. Sinsheimer, Biochim. Biophys. Acta, 149, 476 (1967). % Radloff, R., W. Bauer, and J. Vinograd, these Procegpings, 57, 1514 (1967). ’ 9 Goulian, M., and A. Kornberg, these Procegpines, 58, 1723 (1967). VoL. 60, 1968 BIOCHEMISTRY: COZZARELLI ET AL. 999 10 Kleinschmidt, A. K., D. Lang, D. Jacherts, and R. K. Zahn, Biochim. Biophys. Acta, 61 857 (1962). 11 Inman, R. B., C. L. Schildkraut, and A. Kornberg, J. Mol. Biol., 11, 285 (1965). 12 Mukai, F. H., J. Gen. Microbiol., 23, 539 (1960). 13 Barner, H. D., and 8S. 8S. Cohen, Biochim. Biophys. Acta, 30, 12 (1958). 4 Stern, J. L., M. Sekiguchi, H. D. Barner, and 8. 8. Cohen, J. Mol. Biol., 8, 629 (1964). % Studier, F. W., J. Mol. Biol., 11, 373 (1965). 16 Vinograd, J., and J. Lebowitz, J. Gen. Physiol., 49, 103 (1966). 17 Inman, R. B., J. Mol. Biol., 25, 209 (1967). 18 Lang, D., H. Bujard, B. Wolff, and D. Russel, J. Mol. Biol., 23, 163 (1967). 19 Sinsheimer, R. L., J. Mol. Biol., 1, 43 (1959). 2 Clayton, D. A., and J. Vinograd, Nature, 216, 652 (1967). 21 Roth, T. F., and D. R. Helinski, these Proceepines, 58, 650 (1967). 22 Rush, M. G., A. K. Kleinschmidt, W. Hellman, and R. C. Warner, these PRocEEDINGs, 58, 1676 (1967). 23 Schildkraut, C. L., J. Marmur, and P. Doty, J. Mol. Brol., 4, 430 (1962). 24 The half-width of the plasmid DNA band is 1.56 times that of 6X 174 RF, measured under the same conditions. The calewlated ratio of molecular weights is therefore 2.43 (Meselson, M., F, W. Stahl, and J. Vinograd, these ProceEepinos, 43, 581 (1957)), in good agreement with that determined by electron microscopy. % Bode, V. C., and A. D. Kaiser, J. Mol. Biol., 14, 399 (1965). 2¢ J. Wang has found that the tertiary structures of ¢X174 RFI and plasmid DNA are relaxed by the same number of molecules of ethidium bromide per unit length of DNA (personal communication). . 7 Cairns, J., in Cold Spring Harbor Symposia on Quantitative Biology, vol. 28 (1963), p. 43. % Young, E. T., Il, and R. L. Sinsheimer, J. Mol. Biol., 30, 147 (1967). 29 Isolated from strain TAU after two growth cycles in the presence of 35 ug/ml acridine orange, followed by thymidine deprivation. * Hanawalt, P. C., Nature, 198, 286 (1963). 31 Barner, H. D., and S. 8. Cohen, J. Bacteriol., 68, 80 (1954). 32 Matsubara, K., A. Taketo, and Y. Takagi, J. Biochem. (Japan), 54, 225 (1962). 33 Tshibashi, M., and Y. Hirota, J. Bacteriol., 90, 1496 (1965). 34 Melechen, N. E., and P. D. Skaar, Virology, 16, 21 (1962). % Lindqvist, B. H., and R. L. Sinsheimer, J. Mol. Biol., 28, 87 (1967). 36 A strain lacking endonuclease I isolated by P. H. Flanders. 7 Roepke, R. R., R. L. Libby, and M. H. Small, J. Bacteriol., 48, 401 (1944). % Roepke, R. R., J. Bacteriol., 93, 1188 (1967). 39 The exposure of THU to 900 ergs mm~? of UV light, sufficient to initiate cell lysis within 1 hr, did not cause any change in the amount of plasmid DNA. Jacob, F., S. Brenner, and F. Cuzin, in Cold Spring Harbor Symposia on Quantilative Biology, vol. 28 (1963), p. 329. “| Hickson, F. T., T. R. Roth, and D. R. Helinski, these Proceevines, 58, 1731 (1967). 42 Rownd, R., R. Nakaya, and A. Nakamura, J. Mol. Biol., 17, 376 (1966). 48 Nomura, M., Ann. Rev. Microbiol., 21, 257 (1967). 44 Yudelevich, A., and M. Gold, Federation Proc., 26, 450 (1967). * Thomas, C. A., and L. A. MacHattie, Ann. Rev. Biochem., 36, 485 (1967).