Biochimica et Biophysica Aaeta, 335 (1974) 123-138 Elsevier Scientific Publishing Company, Amsterdam - Printed in The Netherlands

BBA 97910

EFFECTS OF t DEVELOPMENT ON TEMPLATE SPECIFICITY OF

E S C H E R I C H I A C O L I RNA POLYMERASE

ARNOLD BROWN* and STANLEY N. COHEN**

Department of Medicine, Stanford University Medical Center, Stanford, Calif. 94305 (U.S.A.)

(Received September 4th, 1973)

SUMMARY

Treatment of bacterial cell extracts with micrococcal nuclease and subsequent inhibition of nuclease activity by addition of EDTA and 3', 5'-thymidine diphosphate was used to achieve DNA-dependent RNA synthesis without resorting to enzyme fractionation. Following heat induction of t CI857 lysogens or infection by 2, a 4--5-fold selective stimulation of transcription of 2 DNA by nuclease-treated crude extracts was observed. Extracts isolated from non-lysogenic bacteria, uninduced lysogens, and N - mutants copied 2 and Escherichia coli DNA templates almost equally; however, mutation of the Q gene did not affect the t-dependent transcription activity. The t-dependent activity is sensitive to inhibition by rifampicin, and co- purifies with the E. coli enzyme through (NH4)2SO4 fractionation and low-salt glycerol gradient centrifugation steps. However, the altered activity is highly labile, and is lost following high-salt glycerol gradient centrifugation. Experiments employing various deletion mutants suggest that the genes involved in determining this activity are located between exo and CIII.

INTRODUCTION

The sequential expression of viral genetic information during development of bacteriophage 2 is regulated largely at the level of gene transcription, t lytic growth also causes partial shut-off of host bacterial nucleic acid and protein synthesis [9-14] and the consequent preferential production o f t gene products during phage develop- ment. This phenomenon is less well understood, but earlier experiments [13, 14] suggest that transcriptional control mechanisms may also play a role in this process.

Recently, experiments by several groups have sought to identify either a 2-specific RNA polymerase or another t gene product having the ability to alter the

Abbreviation: TEMD, 0.02 M Tris-HCl, pH 7.9, 0.001 M EDTA, 0.1 M MgCI2 and 0.1 mM dithiothreitol. SSC, 0.15 M NaCI-0.015 M trisodium citrate, pH 7.0.

* Present address: Department of Medicine, University of Pittsburg School of Medicine and USA Hospital, Pittsburg, Pa. 15420 (U.S.A.).

** Please address reprint requests to this author.

124

template specificity of the Escherichia coli RNA polymerase, either qualitatively or quantitatively. In other phage systems, alteration of host transcriptional specificity following phage infection has been shown to occur as a result of: (1) synthesis of an ancillary RNA polymerase factor (e.g. tr) [15-20]; (2) alteration of the host "core" RNA polymerase [21-23] and (3) production of a new RNA polymerase coded for by the phage genome [24-28]. In the case of 2, the key roles of the N and Q genes in regulating phage transcription have long been recognized from genetic and bio- chemical studies [2-4, 6, 7, 30, 31]. In addition, more recent in vitro experiments by Naono and Tokuyama [32] have implicated the Q gene product in the control of transcription from regions of the 2 genome involved in "late" bacteriophage functions. Reports by Georgopolous [33], Greenblatt [34] and Dotkin and Pearson [35] have directly implicated the 2 N protein in the transcriptional control of 2 development.

In order to achieve 2 RNA synthesis that is dependent upon the addition of exogenous DNA [6, 36, 37] most earlier studies of transcription of 2 DNA in vitro have utilized purified RNA polymerase preparations. Although such preparations still show the preference for regions of the 2 genome involved with early phage func- tions that is seen in vivo, certain of the enzymes or factors involved in transcriptional control may have been lost in the course of purification. In an attempt to duplicate the in vivo environment, the present experiments have employed an in vitro RNA- synthesizing system that is initially unfractionated, but is almost entirely dependent on exogenously added DNA template. The results of these studies indicate that altera- tion of both the specificity and activity of host RNA polymerase occurs during development of phage 2, and that a 2-specific gene product is involved in this process. A preliminary report of this work has appeared [38].

MATERIALS AND METHODS

Materials Bacterial and phage strains are listed in Table I. Nucleoside triphosphates

were obtained from either Sigma Chemical Co. or Calbiochem. 2-Phosphoenol- pyruvate, thymidine-3', 5'-diphosphate, rifampicin, and dithiothreitol were obtained from Calbiochem. [3H]UTP was purchased from Schwartz Bioresearch. Micrococcal nuclease (EC 3.1.4.7) was obtained from either Worthington Biochemical Corp. or P-L Laboratories. Chioramphenicol was a gift from Mann Research. Other chemicals used were standard reagent grade.

For most experiments, bacteria were grown at 34 °C in broth containing 1 ~o typtone (Difco), 0.5 ~ yeast extract (Difco), 0.5 ~ NaC1, 0.01 M Tris-HCl, pH 7.5, 1 mM MgSO4 and 0.5 ~ glycerol. Lysogens were induced at A65o, m 0.6 (approx. 6 • 10 s bacteria/ml) by raising the temperature of the culture to 42 °C for 10 min and were then incubated at 37 °C for another 10 min prior to harvesting. Cells were rapidly chilled, sedimented, washed in 0.02 M Tris-HC1, pH 7.9, 0.001 M EDTA, 0.1 M MgClz and 0.1 mM dithiothreitol (TEMD buffer) and resuspended in 1/100 of the original culture volume in the same buffer containing 10 ~o glycerol. Cell suspensions were then sonicated for three bursts of 15 s each, using a Branson sonica- tor at an energy of 75-80 W, and sonicates were centrifuged at 100 000 × g for 30 min. Following centrifugation, the supernatant was incubated at 34 ° C with micrococcal nuclease (450 units/ml) for 10 min in the presence of 0.1 M CaC12; 2-phosphoenol-

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126

pyruvate was then added (final concentration 25 mM) and the mixture was incubated for an additional 5 min. Inhibition of nuclease activity was accomplished by addition of thymidine-3', 5'-diphosphate (10 mM) and EDTA (50 mM). Except for incuba- tions, all operations were performed at 4 °C. In certain experiments, 2 CI857 lysogens grown at 34 °C in 100-1 batches in a FermaceU unit (New Brunswick Scientific) were thermally induced (42 °C for 10 min), and were harvested after a further 10 min of incubation at 37 °C using a Sharples continuous-flow refrigerated centrifuge. Non- lysogenic E. coli control bacteria were treated similarly. Bacterial cells were stored frozen at --70 °C until used. Frozen cells were ground with alumina (Alcoa, A-305) and resuspended in TEMD buffer containing 10 ~ glycerol. Following low-speed centrifugation to remove the alumina and cell debris, cell grindates were treated as described above for sonicates. Extracts of the non-lysogenic E. coli strain A19 or uninduced lysogens were used as controls, as indicated in specific experiments; both kinds of controls gave similar results.

Infection of bacteria with ;~ mutants was carried out at a multiplicity of 5, as previously described [13]. Following phage adsorption at 4 °C for 10 min, infected bacteria were incubated for an additional 20 min at 37 °C and were then harvested and treated as described above.

RNA polymerase reaction mixtures (0.1 ml) contained 0.04 M Tris-HC1, pH 7.9, 0.01 M MgCI2,0.1 M KC1, 0.1 mM dithiothreitol, and 0.8 mM each of ATP, CTP, GTP and [3H]UTP (spec. act., 12 Ci/M), and 50-100 pg of protein. Assays were incubated at 34 °C for 20 min, rapidly chilled, and 2 ml of cold 5 ~o trichloro- acetic acid containing 0.1 M soldium pyrophosphate and unlabeled UTP carrier (50 #g/ml) was immediately added to each. Precipitates were collected on GF/C glass fiber filters, which were washed, dried, and counted as previously described [36]. Each sample was assayed in duplicate in every experiment, and the values reported represent the mean result; in general, duplicates agreed within 10 ~.

;~ phage DNA and bacterial DNA were prepared by methods previously described [36]. The DNA of phages T7, T4 and ~b80 were gifts from P. Loban, T. R. Broker and C. Yanofsky, respectively. 3H-Labeled SV40 DNA was obtained from P. Berg. Calf thymus DNA was purchased from Worthington Biochemical Corp. and was further purified by extraction 2-3 times with redistilled phenol [36] equilibrated with 2 × SSC (0.15 M NaCI-0.015 M trisodium citrate, pH 7.0).

RESULTS

Effects of micrococcal nuclease on DNA dependence of crude bacterial extracts Table II shows the effects of micrococcal nuclease treatment on DNA-depen-

dent RNA synthesis by crude bacterial extracts prepared from non-lysogenic E. coli strain AI9. As seen in this table, RNA synthesis by the untreated preparation is maximally stimulated only 2-fold by addition of exogenous DNA, whereas pre- treatment of extracts with micrococcal nuclease leads to a 20-fold stimulation by similar amounts of added DNA. Prior to use of nuclease-treated extracts for the synthesis of RNA, the nuclease was inhibited by addition of thymidine-3',5'-diphos- phate, and concurrent chelation of Ca z + by addition of EDTA. As seen in Table III, this procedure resulted in effective inhibition of nuclease activity.

127

TABLE II

EFFECTS OF NUCLEASE TREATMENT ON DNA DEPENDENCE OF CRU D E BACTERIAL EXTRACTS

Crude enzyme was prepared from non-lysogenic 17. coli strain A19 as described in Materials and Methods except that a portion of the crude extract was not treated with nuclease. RNA synthesis was measured using the standard assay described in Materials and Methods. Values are pmoles UTP incorporated/20 rain incubation per mg protein.

No Nuclease Treatment Nuclease Treated

A. Crude bacterial extract 1530 337 B. Crude e x t r a c t + D N A 3007 6556 C. Stimulation by DNA (B/A) 2.0 19.5

TABLE III

EFFECTS OF 3 ' ,5 ' -THYMIDINE DIPHOSPHATE ON MICROCOCCAL NUCLEASE ACTIVI- TY IN CRUDE EXTRACTS

Crude extracts were prepared from non-lysogenic E. coli A 19 as described in Materials and Methods except that the extract was divided into three aliquots prior to assay of micrococcal nuclease activity by solubilization of 1 +C-labeled E. coli DNA. The first was untreated (no nuclease or Ca 2+) and had no EDTA or inhibitor (3',5'-thymidine diphosphate) added. The second was treated with nuclease and Ca 2 + but EDTA and inhibitor were omitted. The third was treated completely as described. The extracts were then added to a standard RNA polymerase assay mixture except that ~ +C-labeled E. coli DNA was added instead of 13HIUTP. The mixture was incubated for 20 rain at 34 °C, then precipi- tated with cold 5 % trichloroacetic acid and filtered through Whatman GF/C filters. The filters were dried and counted in a toluene-based scintillation fluid.

A. No nuclease 1+C-Labeled E. coli 1634 DNA precipitable (cpm)

B. Nuclease ÷ C a 2+ 32

C. Nuclease+Ca 2+ q-EDTAq-3' ,5 '- 1734 Thymidine diphosphate

Effects of 2 phage mutants on RNA polymerase activity The effects of development of various 2 mutants on the RNA polymerase

activity of crude bacterial extracts and on the specificity of transcription are shown in Table IV. As seen in this table, an increase in the specific activity of RNA poly- merase in crude bacterial extracts was observed following heat induction of a 2CI857Ram5 lysogen, using both calf thymus DNA and ). DNA as templates. In contrast, no significant change in the ability of bacterial extracts to transcribe E. coli DNA was seen following phage induction. Induction of an su- 2 CI857Nam7am53 lysogen had no effect on the activity of bacterial extracts, suggesting that the observed 2-related alteration in RNA polymerase activity was dependent on normal functioning of the 2 N gene; furthermore, the 2 nin5 mutation, which renders the operon containing the Q gene independent of N-gene function and consequently permits normal late phage development, did not restore the ability to alter host RNA polymerase activity to the N - phage.

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A polar mutation in the x region of 2 (i.e. x13), which prevents transcription of early phage genes located immediately to the right of the immunity region [3, 6] or an amber mutation in the Q gene, which renders the phage unable to make late messenger RNA [31], did not influence synthesis of the product(s) responsible for appearance of 2-specific transcription activity (Table IV). The specificity for ). DNA produced by cro- mutants which have been shown to overproduce the products of genes to the left ofcI, as well as the cI product itself [39], was not significantly different than that observed with cro ÷ phage. Induction of WGS5, which carries a 2 segment that includes the phage genes to the left of N, but is lacking the genes to the right of the x region, leads to a prominent increase in 2-specific RNA polymerase activity and a pronounced preference for transcription of 2 DNA. In contrast, deletion of genes to the left of N, as in WGS6, a derivative of WGS5, totally prevented the appearance of the 2-specific transcription activity (Table IV).

The above results indicate that N-gene function is necessary but not sufficient for production of 2-specific transcription activity. In addition, the expression of genes to the left of N is essential for this activity; genes transcribed to the right of cI are not involved and 2 DNA replication is not required.

The results shown in Table V are consistent with this interpretation. Altered RNA polymerase activity with 2 DNA template is seen following infection of E. coli

AI9 by 2pbio 7-20, which lacks only a relatively short segment of phage DNA to the left of 6 (Fig. 1). However, the 2 mutants pbiol0 and pbio252, which carry longer deletions of the phage genome that terminate in or just to the left of gene CIII, fail to synthesize the substance responsible for altered transcriptional activity.

TABLE V

EFFECTS OF 2 INFECTION ON ENZYME ACTIVITY OF CRUDE LYSATES Units are pmoles UTP incorporated/20 rain per mg protein. Extracts were prepared and assayed as indicated in Materials and Methods. Expts 1 and 2 were carried out at widely separated times.

Source of DNA template Ratio enzyme Calf thymus E. coli 2 2/coli

Expt I No infection 4 384 889 1017 0.8 ClamR5 13 986 896 3548 4.0 CI857pbiolO 4 774 1163 909 0.8 Clpbio7-20 6 620 403 3080 7.6

Expt 2 No infection 9 245 1415 2380 1.7 ClamR5 17 200 637 5800 9.1 C1857pbio252 7 920 884 1815 2.1

Transcription of various DNA templates by RNA polymerase preparations isoiated from induced 2 lysogens or from control bacteria is compared in Table VI. As seen in this table, the ability of the enzyme preparations to transcribe E. eoli DNA, phage T7 DNA and ~b80 is essentially unchanged following 2 induction; there is a moderate stimulation of the transcription of T4 DNA and calf thymus DNA associat- ed with 2 development. However, the most prominent alterations in template efficiency as a consequence of 2 induction are seen with 2 DNA as template.

130

p bio 10

p bio 2.52

pb io 7-20

¢P ~ o 7~ W G 5 . 5 WG.S 6

Fig. 1. Genetic map of a portion of the right arm of the bacteriophage 3, chromosome. The basis for assignment of various markers and pbio deletions to specific location has been cited previously [13, 14]. The shaded bars opposite thepbio designations represent the deleted segment in these phages. On the other hand the terminated lines opposite the WGS designations represent the extent of the phage fragment inserted into the F'trp episome carried by the strain (reference and personal commu- nication). This diagrammatic map is not drawn to scale,

TABLE VI TEMPLATE SPECIFICITY OF }t-DEPENDENT TRANSCRIPTION ACTIVITY Values are pmoles UTP incorporated ]20 rain incubation per mg protein. Techniques are described in Materials and Methods. E. coli strain A19 (}tCI85Ram5) was used as the source of enzyme.

DNA template Source of enzyme Ratio Induced/uninduced

Uninduced Induced lysogen lysogen

Calf thymus 4 660 13 800 2.96 E. coli 300 462 1.54 }t 574 5 020 8.75 T7 30 500 53 000 1.74 T4 6 900 23 700 3.40 ~b80 2 075 1 780 0.86

Effects of ehloramphenicol and rifampicin on ;L-specific transcription activity The observed effects of ;L development on RNA polymerase activity and

template specificity are prevented by addition of chloramphenicol (200 #g/ml) to lysogenic cultures 10 min prior to phage induction (Table VII), supporting the view that ;t genetic expression is involved in these effects. As seen in this table, enzyme preparations obtained from chloramphenicol-treated cultures showed no preference for 2 DNA, as compared with E. coli DNA. Moreover, both the baseline E. coli RNA polymerase activity and the ;L-specific chloramphenicol-sensitive increment were equally inhibited by rifampicin (Table VIII).

Purification of 2-specific transcription activity Purification of the RNA polymerase activity from an induced lysogen by

(NH4)2SO 4 fractionation and subsequent centrifugation in low-salt gradients was associated with an increasingly prominent preference for ;L versus E. coli DNA (Table IX). Little change occurred in the pattern of transcription during purification

131

TABLE VII

EFFECT OF CHLORAMPHENICOL ON 2-DEPENDENT ACTIVITY FROM AN INDUCED LYSOGEN

Values are pmoles UTP incorporated/20 min incubation per mg protein. E. coli Al9 lysogenic for 2CI857Ram5 was grown at 34 °C to A6so ~,~ 0.6 as previously described. The culture was then divided in two, and chloramphenicol (200/tg/ml) was added to one portion. Both were then incubated for another l0 min at 34 °C at which time both were agitated for l0 min at 42 °C then at 37 °C for l0 min at which time they were harvested and prepared as indicated in Materials and Methods.

DNAtemplate No chloramphenicol 200pg/ml chloramphenicol

Calfthymus 31 900 8 140 E. coH 2 600 1 670 2 10 400 1 465 None 188 0

TABLE VIII

EFFECT OF RIFAMPICIN ON THE 2-DEPENDENT TRANSCRIPTION ACTIVITY

Values are pmoles UTP incorporated/20 rain incubation per mg protein. Crude enzymes were pre- pared and assays carried out as indicated in Materials and Methods and Table VII. For each enzyme preparation duplicate assay systems were prepared: Rifampicin (2/~g/ml) was added to one reaction mixture prior to the addition of the enzyme.

DNA template Non-lysogen Induced lysogen

No +2/~g/ml Inhibition No +2 t~g/ml Inhibition rifampicin rifampicin (~) rifampicin rifampicin (9/00)

Calfthymus 1803 83 96 7370 141 98 1551 45 97 6785 159 98

None 71 148 9 88

of enzyme p repa ra t ions ob ta ined f rom non- lysogenic cont ro l bacter ia . As seen in Fig. 2, the enzyme act ivi ty assayed direct ly f rom fract ions o f the low-sal t glycerol gradient o f the induced lysogen was mos t active with ;~ D N A template , and had very litt le act ivi ty using E. coli D N A . However , when the several f ract ions mak ing up the glycerol g rad ien t peak were poo led and reprecip i ta ted with (NH4)2SO 4, 2-specific t ranscr ip t ion became less p rominen t , as shown in Table IX. The enzyme peak o f the non- lysogen showed typical " c o n t r o l " act ivi ty in all (NH4)2SO 4 and glycerol gradient fract ions.

R N A po lymerase isola ted f rom induced 2 lysogens con t inued to pur i fy th rough low- (Fig. 2) and high-sal t glycerol gradients with p repa ra t ions isola ted f rom uninduc- ed or non- lysogenic bacteria. However , enzyme p repa ra t ions ob ta ined f rom induced lysogens no longer demons t r a t ed a specificity for 2 D N A after cent r i fugat ion in high- salt glycerol gradients. The lost specificity could no t be res tored by combin ing fract ions f rom these gradients .

Enzyme p repa ra t ions tha t were reprec ip i ta ted fol lowing poo l ing o f the princi- pa l act ivi ty peak fract ions f rom the low-sal t glycerol gradient were examined for poss ible nuclease act ivi ty in o rder to de termine whether D N A degrada t ion was

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Fig. 2. Glycerol gradients (low salt) were prepared as described in the legend of Table IX. Fractions were collected with an ISCO refrigerated fraction collector. The protein concentration of the fraction was estimated by the Warburg-Christin technique by measuring the absorbance at 280 and 260 nm. Enzyme assays were performed as previously described, cpm × 10-a represents UTP incorporation per 20 rain incubation at 34 °C. • - - - • , protein concentration. A_ A, enzyme assay with calf thymus DNA. O- - -O, enzyme assay with 2 DNA. A- - -A, enzyme assay with E. coli DNA.

Fig. 3. Circular all-labeled SV40 DNA was incubated in a 0.05-ml reaction mixture containing 0.04 M Tris-HC1, pH 7.9, 0.01 M MgCl2.0.1 M KCI, 0.2 mM dithiothreitol, 1 mM ATP and 10 mg bovine serum albumin. No further additions were made to one reaction mixture and 0. I ng pancreatic deoxyribonuclease was added to a second. The third received 6.2/zg of the low-salt glycerol gradient purified extract from the non-lysogen. The last received 15/zg of the preparation from the induced lysogen. All were incubated for 20 rain at 34 °C at which time 10/d each of 0.5 M EDTA and 1 M NaOH were added. The mixtures were then layered on 5.2-ml 10--30 % alkaline sucrose gradients containing 0.1 M NaOH, 0.9 M NaCl and 1 mM EDTA. The gradients were centrifuged for 90 rain at 40 000 rev./min in the SW50.1 rotor o f a Spinco L2-65B ultracentrifuge at 20 °C. 8-drop fractions were collected directly on 2.2-cm circles of Whatman No. 3 filter paper. The filters were dried, washed, in bulk in 5 % trichloroacetic acid for 5 min with gentle agitation, washed in 100 % ethanol and then dried and counted. Values given are total counts recovered in Peak 1 (Component 1, covalently closed circles) and Peak II (Component 2, open (nicked) circles or linear molecules), respectively.

i n v o l v e d in t he o b s e r v e d ; t - d e p e n d e n t t r a n s c r i p t i o n act ivi ty, a l l - L a b e l e d 2 D N A was

i n c u b a t e d w i t h e n z y m e f r a c t i o n s u n d e r c o n d i t i o n s s imi la r to t h o s e e m p l o y e d fo r t he

134

RNA polymerase assay. As seen in Table X, no solubilization of labeled DNA was detected using the technique of Geiduschek and Daniels [40]. In addition, enzyme preparations were incubated with 3H-labeled circular SV40 DNA [41 ], and this DNA was subsequently centrifuged in alkaline sucrose gradients to determine the extent of covalently closed circularity. As seen in Fig. 3A, 36 ~ of the SV40 DNA sedimented as closed circular DNA in 10-30 ~ alkaline sucrose gradients prior to treatment with enzyme preparations from ~.-induced or control cells. Incubation of DNA with enzyme obtained from either the non-lysogenic E. coli strain or from an induced 2Ram lysogen caused no shift from the covalently closed circular peak (Peak 1) to the non-covalently closed circular peak (Peak 2). Pancreatic deoxyribonuclease (0.1 ng) added to the incubation mixture degraded the SV40 DNA, so that only fragments remained.

TABLE X

NUCLEASE ASSAY

Denatured 3H-labeled ~ DNA (diluted with cold DNA so that 1500 cpm represented approx. 10 nmoles of DNA) was incubated with either the glycerol gradient enzyme from the non-lysogen or induced lysogen or with pancreatic deoxyribonuclease as indicated. The control had no enzyme addi- tion. The volume of the reaction mixture was 0.25 ml and contained 20 mM Tris-HC1, pH 7.9, 10 mM MgCI2, 100 mM dithiothreitol, 80 mM ATP and 50/*g bovine serum albumin (Sigma). The mixture was incubated for 20 min at 34 °C at which time 10 ml of 0.5 M KC1-0.01 M Tris, pH 7.5, -0.01.M EDTA buffer was added. The solution was filtered through Schleicher and Schueil B6 nitrocellulose membrane filters which were then washed with 50 ml of the same buffer, dried and counted.

Additions Retention of acid precipitable 3H-labeled 3, DNA (cpm)

None 1430 Pancreatic deoxyribonuclease 0.1 g 16 Enzyme from non-lysogen 1381 Enzyme from induced lysogen 1334

Fractions comprising the enzyme peaks obtained from the low- and high-salt glycerol gradients were subjected to electrophoresis on 7.5 ~o polyacrylamide-sodium dodecylsulfate gels according to the technique of Shapiro et al. [42]. Fig. 4 shows typical densitometer tracings of such gels. The subunits that have previously been shown to be components of the E. coli RNA polymerase (i.e. ~, [3/~', o) [43, 44] were easily identifiable on all gels, whether the enzyme was obtained from non-lysogenic E. coli or from the induced lysogen. In addition, the molecular weights and molar mass ratios of the RNA polymerase subunits were unaltered by ,~ induction, as shown by the similar electrophoretic mobility of the subunits and the size of peaks obtained from the induced vs control enzymes. In addition to the previously described compo- nents of E. coli RNA polymerase, enzyme preparations obtained by treatment of crude bacterial extracts with micrococcal nuclease and subsequent purification by ( N H 4 ) 2 S O 4 and low-salt glycerol gradient centrifugation contained significant amounts of peptides of 115 000-120000, 72000 and 60 000 mol.wts as well as variable amounts of peptides having lower molecular weights. A significantly greater amount of the 72 000 mol. wt fraction was observed in enzyme preparations obtained from the lysogen, as compared with preparations isolated from non-lysogenic E. coli

135

i ~ I I I I ~ l I L I I I

~E ~N°n'l~8~en 1o " N°n'lvG°gen

II, 0 2 4- 6 8 l0 0 2 4- 6 G 10

Cm Fig. 4. The enzymes in 0.01 M sodium phosphate buffer (pH 7.2) containing 1 ~ sodium dodecyl- sulfate, 1 ~ mercaptoethanol and l0 ~ glycerol were heated for 2 min at 100 °C. Bromphenol blue was added as a marker dye and the mixture was layered onto 10-cm 7.5 ~ polyacrylamide gels made in 0.1 M sodium phosphate (pH 7.2) with 0.1 ~ sodium dodecylsulfate. Gels were electrophoresed at 90 V (constant voltage) at room temperature until the tracking dye had migrated to the end of the gel. The gels were then removed from the glass tubes in which they had been electrophoresed and were fixed overnight in 20 ~ sulfosalicylic acid. They were then stained with 0.25 ~ Coomasie brilliant blue for 3 h. The gels were de-stained by repeated changes of 7.5 ~ acetic acid-5 ~ methanol in which they were subsequently stored. Stained gels were scanned in a Gilford spectrophotometer with a gel scanning attachment at a wavelength of 560 nm.

or from uninduced 2 lysogens. The 72 000 tool. wt peptide was not seen following additional purification of the enzyme by centrifugation in high-salt glycerol gradients. Attempts to further purify this fraction, which appeared to be associated with the 2-dependent activity, by phosphocellulose chromatography were unsuccessful.

DISCUSSION

The degradation of endogenous DNA in crude bacterial extracts by addition of micrococcal nudease, and the subsequent specific inhibition of nuclease activity has proved to be an effective means of obtaining bacterial cell extracts that are un- fractionated but that are nevertheless dependent upon addition of exogenous DNA template for RNA synthesis. In addition, use of a variation of the system described here for achieving DNA-dependent protein synthesis (Brown, A., Chang, A.C.Y. and Cohen, S. N., unpublished) suggests that the procedure may prove to be generally useful in studies of nucleic acid and protein synthesis by unfractionated extracts of both bacterial and animal cells.

136

Our results indicate that a change in the specific activity and transcription pattern of the E. coli DNA-dependent RNA polymerase normally occurs following induction of 2 prophage, or following external infection of the host by mature 2 virus. This change requires new protein synthesis, and specifically involves expression of a 2 gene or genes located to the left of N. The phage region involved is defined by its presence in ipbio 7-20 but its absence in 2pbio deletion mutants extending into or beyond gene CIII (i.e. 2pbiolO, 2pbio 252).

Since N plays a fundamental role in controlling the expression of early genes [2, 3, 6-8, 31 ] it has been suggested that N may interact with the RNA polymerase itself [33, 45] to affect either its specificity of initiation or its termination sites [37]. More recently, direct biochemical evidence that N is important in controlling the transcription of i DNA has been presented [34, 35, 46].

The results indicate that the expression of the N gene in the absence of the essential product(s) produced by the gene(s) to the left of N is not sufficient to produce the altered RNA polymerase activity. The inability of N mutations to alter the trans- cription activity of the E. coli RNA polymerase may be secondary to the requirement for the N gene product for expression of other phage genes to its left; alternatively, interaction of the N gene product with the product of another gene located to its left may be required to alter the template specificity of the host RNA polymerase.

RNA polymerase isolated from the induced 2 lysogens co-purified through several stages of purification with the enzyme obtained from non-lysogenic cells. In addition, enzymes from either non-lysogenic bacteria or induced lysogens are equally sensitive to inhibition by rifampicin. Both of these observations suggest that the l-dependent product modifies the template specificity of the host enzyme without altering its subunit structure. The relative increase in size of the 72 000-mol. wt polypeptide peak present in induced enzyme purified through low-salt glycerol gradients is of some interest in this regard. A polypeptide of similar molecular weight was observed to be present in RNA polymerase preparations purified from induced lysogens by Vogt [47].

The 72 000-mol. wt polypeptide was not seen following further purification of enzymes (i.e. after the high-salt glycerol gradient); this loss was accompanied by a loss of the k-specific altered transcription activity. Polypeptides of this molecular weight were present in high-salt gradient fractions which sedimented slower than the RNA polymerase peak (unpublished data). However, recombining the various high- salt gradient fractions did not restore the ability of the enzyme to preferentially transcribe 2 DNA. Peptides of this size have not been described associated with genes in the "N operon" [48]. However, the proteins associated with the genes N and CIII were not observed by the methods used. It is also possible that the 72 000-mol. wt peptide is of host origin (such as M factor) [49] but is present in increased amounts as a result of the action of a 2 gene product. A third possibility is that gel pattern difference is unrelated to the activity we have observed.

Earlier experiments by Cohen and Chang (ref. 14 and unpublished data) indicated that no significant solubilization or change in sedimentation characteristics of bacterial host DNA occurs following infection with phage 2. In vitro experiments reported here also show no detectable endo- or exonuclease activity in partially purified RNA polymerase preparations isolated from either the induced 2 lysogen or non-lyogenic E. coli (Table IX and Fig. 3). Based on these data, it appears unlikely

137

that a phage-induced nuclease is responsible for the altered transcription specificity reported here.

Al though the specificity o f the increase in 2-induced transcription activity was not absolute, the greatest proport ional enhancement o f activity was seen when 2 D N A was used as template. Less prominent relative increases in transcription secondary to 2 development were also seen using calf thymus or phage T4 D N A templates, but no significant effects were seen in E. coli D N A or with the phage T7 or q580 D N A .

The 2-induced transcription activity described here differs f rom that reported by N a o n o and Tokuyama [32] in that the activity we have observed is not dependent on Q-gene function (Table IV), and the R N A synthesized in vitro using our system does not show (unpublished data) selective hybridization to the late regions o f 2 D N A .

The activity we have observed may result f rom the presence of a previously undescribed factor which stimulates the preference of the E. coli R N A polymerase for 2 promot ion; the location o f the genes responsible for this activity suggests that it may be related to the previously described 2 genes whose expression results in an inhibition o f host macromolecular synthesis (Hin function) by phage 2 [14].

ACKNOWLEDGMENTS

We gratefully acknowledge gifts of bacterial strains and certain D N A prepara- tions f rom P. Loban, L. Reichardt, W. G. Spiegelman, N. Franklin, T. R. Bioker, C. Yanofsky and A. D. Kaiser. We are also grateful to D. Bert and C. Georgopoulos for helpful discussion of the manuscript. These studies were supported by Grants E-532 and V-50 f rom the American Cancer Society. A.B. is a recipient o f a Dernham Junior Postdoctoral Fellowship Award (J-146) and S.N.C. is recipient o f a U.S.P.H.S. Career Development Award.

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