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Transcription Termination Factor Rho Activity Is Altered in Escherichia Coli with Sua Gene Mutations (RNA-Dependent Atpase/RNA Polymerase/Polarity) JOHN P

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Transcription Termination Factor Rho Activity Is Altered in Escherichia Coli with Sua Gene Mutations (RNA-Dependent Atpase/RNA Polymerase/Polarity) JOHN P Proc. Nat. Acad. Sci. USA Vol. 72, No. 5, pp. 1725-1728, May 1975 Transcription Termination Factor Rho Activity Is Altered in Escherichia coli with suA Gene Mutations (RNA-dependent ATPase/RNA polymerase/polarity) JOHN P. RICHARDSON, CHRISTOPHER GRIMLEY, AND CAROLYN LOWERY Department of Chemistry, Indiana University, Bloomington, Ind. 47401 Communicated by James D. Watson, February 51, 1975 ABSTRACT Rho factor has been purified from a strain allele for the suA gene have been purified to of E. coli containing the Su78 mutation in the suA gene homogeneity. and assayed in another strain with an amber mutation in The yields in both cases are the same: about 0.12 mg of pro- the suA gene. The rho from the Su78 mutant strain is tein from 20 g of cells, which is similar to yields from other present in normal amounts but has altered termination cells by means of the Roberts purification procedure. The two function; it does not terminate transcription at some sites pure proteins have the same specific activities for the poly(C)- that are recognized effectively by the rho factor from the activated of isogenic wild-type strain. Rho in cells with an amber hydrolysis ATP-20 ,umol of ATP hydrolyzed mutation in the suA gene has been assayed by its RNA- min' per mg-and the same mobilities when electrophoresed dependent ATPase activity. Extracts of cells of this strain on polyacrylamide gels containing sodium dodecyl sulfate (Fig. have only 9% as much of this rho activity as extracts of 1). However, these rho factors differ significantly in their abili- cells of the isogenic wild-type strain. These results suggest ties to depress the yields of RNA synthesized in vitro with that rho is the product of the suA gene. Since mutations in the su,4 gene are known to decrease polar effects of purified RNA polymerases from several DNA templates mutations in other genes, it is also suggested that rho (Table 1). For each DNA, the rho from the 8uA mutant factor is at least partially responsible for polar effects. strain (Su78) reduces the yield of RNA synthesized less than the rho from the cells with the wild-type allele. The magnitude Many nonsense and frameshift mutations in one gene of an of this difference depends on the DNA used. With T4 DNA, operon pleiotropically reduce the level of expression of the the Su78 rho caused only an 8% depression, compared with genes in the operon that lie on the operator-distal side of the the early 50% depression with the wild-type rho. In contrast, mutant gene (1). This polar effect is evident in the levels of with PM2 DNA the Su78 rho caused a 33% depression, both the messenger RNA sequences corresponding to the whereas the wild-type rho still only caused a 50% depression. affected genes and the protein products (2, 3). In Escherichia These differences are not because of limitations in the amount coli, second-site mutations in the suA gene can partially re- of rho used; the reactions were saturated with the rho used in lieve the polar effect of the original mutation without sup- each case. pressing the orignal mutation (4, 5). Since these suA gene Analyses of the effects of these factors on the size of the mutations are recessive to the wild-type allele (5) and since RNA made on T4 and T7 DNA templates confirm the inter- amber (nonsense) 8uA mutations have been found (6), it has pretation that the depression of yields of RNA synthesis given been suggested that the product of the wild-type suA gene is a in Table 1 is an accurate indication of the relative termination protein required for the full polar effect (6). In this paper we activities of the factors. With T7 DNA, for example, the present evidence that the product of the suA gene is the rho sedimentation profile of the RNA synthesized in the absence transcription termination factor. of rho has a peak indicating a sedimentation coefficient of 17.8 Rho factor was first isolated and purified from E. coli K12 S in 1.1 M formaldehyde (Fig. 2), which corresponds to an by Roberts, who showed that it causes specific termination of RNA with a molecular weight of 2.2 X 106 (11). When the rho the synthesis of X RNA molecules in vitro (7). It has since been from the wild-type cells is present, the RNA peak is at 9.8 S, shown that rho is active in terminating transcription from a which corresponds to an RNA with a molecular weight of 0.5 large number of natural DNA templates (8). Roberts also X 106. However, when rho from Su78 is present, most of the showed that rho is not a ribonuclease; it does not cleave or RNA molecules synthesized are much larger than those syn- degrade large, isolated X RNA molecules even in complete thesized in the presence of the wild-type rho; the main peak is RNA polymerase reaction mixtures (7). We now know that it at 16.8 but there are also at 14.5 S and does S, peaks 12.0 S. Thus the not catalyze the degradation of nascent RNA molecules Su78 rho does not terminate T7 transcription at the site recog- either (9). On the other hand, when RNA molecules are pres- nized by the wild-type rho it does ent, factor, although appear to rho does catalyze the hydrolysis of nucleoside triphos- terminate the transcription of some RNA molecules at phates to nucleoside diphosphates and orthophosphate (9). other Although the sites that are reached later by RNA polymerase. significance of this ATPase activity is not yet Although the two rho factors are identical with clear, it can be used respect to for a convenient quantitative assay of rho their poly(C)-activated ATP hydrolysis activities, they do factor. We have used this assay to identify and purify rho show factor from cells different rates of ATP hydrolysis when activated by with mutations in the suA gene. nascent RNA molecules. In complete RNA polymerase reac- RESULTS tion mixtures containing T4 DNA or T7 DNA, only the rho that causes extensive termination also catalyzes the release of The rho proteins from a 8uA - strain isolated by Carter and Pi from [y-32PJATP (Table 2). This observation is consistent Newton (Su78) (10) and an isogenic strain with the wild-type with others we have made (C. L. and J.P.R., unpublished ex- 1725 Downloaded by guest on September 25, 2021 1726 Biochemistry: Richardson et al. Proc. Nat. Acad. Sci. USA 72 (1975) TABLE 1. Termination activity of rho factors from cells with the Su78 mutation and cells with the wild-type allele in the suA gene [3H]UMP Phage incorporated Inhibition DNA Rho (cpm) (%) T4 727 Wild-type 396 46 Su78 670 8 T5 - 2136 Wild-type 1210 43 Su78 1919 10 T7 - 1649 Wild-type 660 60 Su78 1399 15 fd RFI - 1934 Wild-type 554 71 Su78 1064 45 PM2 - 1715 Wild-type 861 50 Su78 1151 33 Each reaction mixture contained 0.04 M Tris HCl (pH 7.9); 0.05 M KCI; 12 mM MgCl2; 0.1 mM EDTA; 0.1 mM dithio- threitol; 0.7 mg/ml of bovine serum albumin; 0.2 mM each of ATP, GTP, and UTP; 0.12 mM [3H]CTP (10 Ci/mol); 0.3 pg of RNA polymerase; 0.8 ug of DNA; 0.08 ug of rho factor, where A B C appropriate, in a final volume of 0.05 ml. After incubation for FIG. 1. Polyacrylamide gel electrophoresis of purified rho 30 min at 370, the reaction was stopped by the addition of 0.4 ml proteins. Rho protein was isolated by the procedure of Roberts of 0.1 M Na4P207 and 0.5 ml of 10% trichloroacetic acid. Precipi- (7) from E. coli strains T82 (Su78) and T83 (suA +) supplied by tated RNA was collected and washed on membrane filters and the Austin Newton. These strains are isogenic P1 transductants of a radioactivity on the dried filters was measured in a toluene-base ilv- derivative of MU118 (ZU118) (13). The original Su78 strain scintillation fluid. The procedures for isolation of RNA polymer- was described by Carter and Newton (10). The proteins were ase (from E. coli B) and DNAs have been described previously electrophoresed in a discontinuous slab gel (22), using a 3.5% (24, 25). Wild-type and Su78 rho are the purified factors de- stacking gel and a 10% running gel of polyacrylamide in the scribed in Fig. 1. sodium dodecyl sulfate/Tris. HC1 buffer system described by Laemmli (23). The proteins were stained with Coomassie brilliant activity for the rho isolated from 20 g of cells with a suA amber blue using the conditions of Laemmli (23); (A) 0.2 pg of rho from mutation (strain 2055) as was found for the rho isolated from T83 (wild-type); (B) 0.1 pug each of rho from T83 and T82 (Su78); 20 g of cells of an isogenic strain (2034) with the wild-type (C) 0.2 pg of rho from T82. allele in the suA gene. In both cases, the rho eluted from the phosphocellulose in a single sharp peak in 0.16 M potassium periments) correlating rho termination activity with its na- phosphate buffer. scent-RNA-dependent ATP hydrolysis activity. For instance, Since the residual level of rho factor in strain 2055 is higher in 0.12 M KCl, the rho from E. coli B no longer terminates the than would be expected for the product of a gene with an transcription of T7 DNA, and the T7 RNA made under these amber mutation, caution must be taken in concluding that rho conditions also does not activate the rho ATP hydrolysis is the product of the suA gene.
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