Deoxyribonucleic acid dependent ribonucleic acid polymerases from two T4 phage-infected systems

Determinants of affinity and activity of the anti-sigma factor AsiA

The AsiA protein is a T4 bacteriophage early gene product that regulates transcription of host and viral genes. Monomeric AsiA binds tightly to the sigma(70) subunit of Escherichia coli RNA polymerase, thereby inhibiting transcription from bacterial promoters and phage early promoters and coactivating transcription from phage middle promoters. Results of structural studies have identified amino acids at the protomer-protomer interface in dimeric AsiA and at the monomeric AsiA-sigma(70) interface and demonstrated substantial overlap in the sets of residues that comprise each. Here we evaluate the contributions of individual interfacial amino acid side chains to protomer-protomer affinity in AsiA homodimers, to monomeric AsiA affinity for sigma(70), and to AsiA function in transcription. Sedimentation equilibrium, dynamic light scattering, electrophoretic mobility shift, and transcription activity measurements were used to assess affinity and function of site-specific AsiA mutants. Alanine substitutions for solvent-inaccessible residues positioned centrally in the protomer-protomer interface of the AsiA homodimer, V14, I17, and I40, resulted in the largest changes in free energy of dimer association, whereas alanine substitutions at other interfacial positions had little effect. These residues also contribute significantly to AsiA-dependent regulation of RNA polymerase activity, as do additional residues positioned at the periphery of the interface (K20 and F21). Notably, the relative contributions of a given amino acid side chain to RNA polymerase inhibition and activation (MotA-independent) by AsiA are very similar in most cases. The mainstay for intermolecular affinity and AsiA function appears to be I17. Our results define the core interfacial residues of AsiA, establish roles for many of the interfacial amino acids, are in agreement with the tenets underlying protein-protein interactions and interfaces, and will be beneficial for a general, comprehensive understanding of the mechanistic underpinnings of bacterial RNA polymerase regulation.

Bacillus subtilis RNA polymerase and its modification in sporulating and phage-infected bacteria

Bacillus subtilis RNA polymerase holoenzyme consists of the subunits beta', beta, sigma, alpha, delta, and omega. In sporulating bacteria and in bacteria infected with phages SP01 and SP82, this enzyme undergoes changes in subunit composition and transcriptional specificity that could play a regulatory role in gene transcription. Sporulating bacteria may contain a specific component that inhibits the activity of the sigma subunit of polymerase probably by interfering with the binding of sigma-polypeptide to core enzyme. The hypothetical inhibitor may be metabolically unstable, since its activity is rapidly depleted from sporulating cells in the presence of chloramphenicol. Inhibition of sigma-polypeptide activity may restrict the transcription of phage DNA an infected sporulating cells. Although lacking the sigma-subunit, RNA polymerase purified from sporulating cells contains sporulation-specific subunits of 85,000 and 27,000 daltons. In SP01-infected bacteria, the sigma-subunit is replaced by phage-induced subunits. Purified enzyme containing the protein product of SP01 regulatory gene 28 directs the transcription of phage middle genes in vitro, while enzyme containing phage-induced polypeptides V and VI preferentially copies late genes. Accurate transcription of middle and late genes in vitro requires the host delta-subunit of polymerase (or high ionic strength) but not sigma-subunit. Phage PBS2 induces an entirely new multisubunit RNA polymerase that specifically transcribes PBS2 DNA in vitro. This enzyme is synthesized de novo after infection and does not arise by modification of the B. subtilis holoenzyme.

Solution structure and stability of the anti-sigma factor AsiA: implications for novel functions

Anti-sigma factors regulate prokaryotic gene expression through interactions with specific sigma factors. The bacteriophage T4 anti-sigma factor AsiA is a molecular switch that both inhibits transcription from bacterial promoters and phage early promoters and promotes transcription at phage middle promoters through its interaction with the primary sigma factor of Escherichia coli, sigma(70). AsiA is an all-helical, symmetric dimer in solution. The solution structure of the AsiA dimer reveals a novel helical fold for the protomer. Furthermore, the AsiA protomer, surprisingly, contains a helix-turn-helix DNA binding motif, predicting a potential new role for AsiA. The AsiA dimer interface includes a substantial hydrophobic component, and results of hydrogen/deuterium exchange studies suggest that the dimer interface is the most stable region of the AsiA dimer. In addition, the residues that form the dimer interface are those that are involved in binding to sigma(70). The results promote a model whereby the AsiA dimer maintains the active hydrophobic surfaces and delivers them to sigma(70), where an AsiA protomer is displaced from the dimer via the interaction of sigma(70) with the same residues in AsiA that constitute the dimer interface.

Bacteriophage T4 MotA and AsiA proteins suffice to direct Escherichia coli RNA polymerase to initiate transcription at T4 middle promoters

Development of bacteriophage T4 in Escherichia coli requires the sequential recognition of three classes of promoters: early, middle, and late. Recognition of middle promoters is known to require the motA gene product, a protein that binds specifically to the "Mot box" located at the -30 region of these promoters. In vivo, the asiA gene product is as critical for middle mode RNA synthesis as is that of the motA gene. In vitro, AsiA protein is known to loosen the sigma 70-core RNA polymerase interactions and to inhibit some sigma 70-dependent transcription, presumably through binding to the sigma 70 subunit. Here we show that, in vitro, purified MotA and AsiA proteins are both necessary and sufficient to activate transcription initiation at T4 middle promoters by the E. coli RNA polymerase in a sigma 70-dependent manner. AsiA is also shown to inhibit recognition of T4 early promoters and may play a pivotal role in the recognition of all three classes of phage promoters.

The asiA gene product of bacteriophage T4 is required for middle mode RNA synthesis

The asiA gene of bacteriophage T4 encodes a 10-kDa peptide which binds strongly in vitro to the sigma 70 subunit of Escherichia coli RNA polymerase, thereby weakening sigma 70-core interactions and inhibiting sigma 70-dependent transcription. To assess the physiological role of this protein, we have introduced an amber mutation into the proximal portion of the asiA gene. On suppressor-deficient hosts, this mutant phage (amS22) produces minute plaques and exhibits a pronounced delay in phage production. During these mutant infections, T4 DNA synthesis is strongly delayed, suggesting that the AsiA protein plays an important role during the prereplicative period of phage T4 development. The kinetics of protein synthesis show clearly that while T4 early proteins are synthesized normally, those expressed primarily via the middle mode exhibit a marked inhibition. In fact, the pattern of protein synthesis after amS22 infection resembles greatly that seen after infection by amG1, an amber mutant in motA, a T4 gene whose product is known to control middle mode RNA synthesis. The amber mutations in the motA and asiA genes complement, both for phage growth and for normal kinetics of middle mode protein synthesis. Furthermore, primer extension analyses show that three different MotA-dependent T4 middle promoters are not recognized after infection by the asiA mutant phage. Thus, in conjunction with the MotA protein, the AsiA protein is required for transcription activation at T4 middle mode promoters.

The asiA gene of bacteriophage T4 codes for the anti-sigma 70 protein

The anti-sigma 70 factor of bacteriophage T4 is a 10-kDa (10K) protein which inhibits the sigma 70-directed initiation of transcription by Escherichia coli RNA polymerase holoenzyme. We have partially purified the anti-sigma 70 factor and obtained the sequence of a C-terminal peptide of this protein. Using reverse genetics, we have identified, at the end of the lysis gene t and downstream of an as yet unassigned phage T4 early promoter, an open reading frame encoding a 90-amino-acid protein with a predicted molecular weight of 10,590. This protein has been overproduced in a phage T7 expression system and partially purified. It shows a strong inhibitory activity towards sigma 70-directed transcription (by RNA polymerase holoenzyme), whereas it has no significant effect on sigma 70-independent transcription (by RNA polymerase core enzyme). At high ionic strength, this inhibition is fully antagonized by the neutral detergent Triton X-100. Our results corroborate the initial observations on the properties of the phage T4 10K anti-sigma 70 factor, and we therefore propose that the gene which we call asiA, identified in the present study, corresponds to the gene encoding this T4 transcriptional inhibitor.

Gene product dsbA of bacteriophage T4 binds to late promoters and enhances late transcription

Gene product 33 of phage T4 is known to be essential in late transcription. Upstream from gene 33 and overlapping its 5' terminal sequence by 20 bp, we identified an open reading frame coding for a binding protein for double-stranded DNA (DsbA). Gene product DsbA is composed of 89 amino acid residues with a Mr of 10376 kDa. We purified this protein to homogeneity from over-expressing cells. Gel retardation assays reveal that it binds to DNA and footprint analyses disclose that it interacts preferentially with T4 late promoter regions. At the sites of binding the protein introduces nicks in double-stranded DNA. In vitro transcription assays performed with T4 late modified RNA polymerase on restriction fragments harbouring a T4 late promoter region prove that gene product DsbA enhances transcription from these promoter regions in the presence of gene product 33. Gene dsbA is distinct from gene das which maps close to this genomic region.

Inhibition of transcription of cytosine-containing DNA in vitro by the alc gene product of bacteriophage T4

The alc gene product (gpalc) of bacteriophage T4 inhibits the transcription of cytosine-containing DNA in vivo. We examined its effect on transcription in vitro by comparing RNA polymerase isolated from Escherichia coli infected with either wild-type T4D+ or alc mutants. A 50 to 60% decline in RNA polymerase activity, measured on phage T7 DNA, was observed by 1 min after infection with either T4D+ or alc mutants; this did not occur when the infecting phage lacked gpalt. In the case of the T4D+ strain but not alc mutants, this was followed by a further decrease. By 5 min after infection the activity of alc mutants was 1.5 to 2.5 times greater than that of the wild type on various cytosine-containing DNA templates, whereas there was little or no difference in activity on T4 HMdC-DNA, in agreement with the in vivo specificity. Effects on transcript initiation and elongation were distinguished by using a T7 phage DNA template. Rifampin challenge, end-labeling with [gamma-32P]ATP, and selective initiation with a dinucleotide all indicate that the decreased in vitro activity of the wild-type polymerase relative to that of the alc mutants was due to inhibition of elongation, not to any difference in initiation rates. Wild-type (but not mutated) gpalc copurified with RNA polymerase on heparin agarose but not in subsequent steps. Immunoprecipitation of modified RNA polymerase also indicated that gpalc was not tightly bound to RNA polymerase intracellularly. It thus appears likely that gpalc inhibits transcript elongation on cytosine-containing DNA by interacting with actively transcribing core polymerase as a complex with the enzyme and cytosine-rich stretches of the template.

Identification of the gene encoding an RNA polymerase-binding protein of bacteriophage T4

One of five bacteriophage T4-specified proteins that bind to host RNA polymerase core has been purified and partially sequenced. A mixed oligonucleotide, based on the amino acid sequence, was used to probe genomic restriction fragments. The gene for this protein, previously designated the 15K protein, has been located between T4 genes 45 and 46 and designated rpbA.

A 5'----3' exoribonuclease of human placental nuclei: purification and substrate specificity

An exoribonuclease that hydrolyzes single-stranded RNA by a 5'----3' mode yielding 5'-mononucleotides has been purified from human placental nuclei. Chromatographic studies of crude placental nuclear extracts suggest that the enzyme is a relatively abundant nuclear RNase. Poly(A) is degraded by a processive mechanism while rRNA is degraded in a partially non-processive manner, possibly because of its secondary structure. The enzyme has an apparent molecular weight of 113,000, derived from determinations of the Stokes radius (43 A) and sedimentation coefficient (6.3 S). Substrates with 5'-phosphomonoester end groups are 10-20 times better than 5'-dephosphorylated substrates. The locale of the enzyme in nuclei of normal human cells as well as its mode of action suggest a role in nuclear RNA processing or turnover.

Changed promoter specificity and antitermination properties displayed in vitro by bacteriophage T4-modified RNA polymerase

A 5.5 X 10(3) base-pair fragment of bacteriophage T4 DNA carrying genes 1, 3, 57, ipI and a cluster of transfer RNA genes was used as template for RNA polymerase isolated from uninfected Escherichia coli and from T4-infected bacteria. RNA transcripts were fractionated by gel electrophoresis and mapped by using as transcription template the 5.5 X 10(3) base fragment cleaved with different restriction enzymes. The comparison of the transcripts synthesized by the two RNA polymerases revealed a dramatic difference in their initiation specificities and abilities to utilize a transcription termination site. The T4-modified polymerase utilizes three new promoters on the template DNA fragment that are not utilized by the host enzyme. The modified enzyme, however, fails to produce some of the transcripts synthesized by the host RNA polymerase. The ability of T4-modified RNA polymerase to terminate transcription at a terminator present in the template DNA fragment is greatly reduced as compared to the unmodified host enzyme. The factors responsible for the new initiation and termination properties are associated with RNA polymerase core component. Analysis of RNA polymerase from bacteria infected with T4 mutants demonstrates that the new promoter specificity and the antitermination effect are caused by different factors.

In vitro transcription of phage T4 late genes on purified DNA by partially purified RNA polymerase from T4-infected Escherichia coli b cells

RNA polymerase was purified from 'late' phage T4-infected Escherichia coli B cells by DNA-cellulose affinity chromatography and high salt agarose filtration. The DNA-cellulose-purified RNA polymerase preparation contained T4-coded DNA endonuclease activity and several proteins, some with sizes comparable with the known T4 maturation factors, essential for late RNA synthesis. Some of these proteins, and the DNA endonuclease utilizing native, parental T4 DNA and supercoiled phi X 174 DNA as substrates, were partially separated from the RNA polymerase as a complex during agarose filtration. In vitro RNA was made by the DNA-cellulose-purified RNA polymerase using native, parental T4 DNA as template. About 26% of the in vitro RNA was transcribed from the DNA r-strand; 75% from the same r-strand region as in vivo late after infection. Both the abundancy and specificity of the in vitro r-strand transcription were markedly reduced after agarose filtration of the enzyme. Addition of the proteins separated from the RNA polymerase during agarose filtration caused a restoration of in vitro r-strand transcription abundance, but not its specificity. These results show that partially purified RNA polymerase from T4-infected E. coli B cells was able to transcribe late T4 genes in vitro with some abundancy and specificity on purified, parental T4 DNA, but further purification of the enzyme caused an irreversible reduction of this ability.

Bacteriophage T4 alc gene product: general inhibitor of transcription from cytosine-containing DNA

The alc gene of bacteriophage T4 was originally defined on the basis of mutations which allow late protein synthesis directed by T4 DNA containing cytosine rather than hydroxymethylcytosine. The question remained whether the normal alc gene product (gpalc) also blocks the transcription of early genes from cytosine-containing DNA. Complementation experiments were performed between hydroxymethylcytosine-containing phage which direct gpalc synthesis but carry mutations in a given gene(s) and cytosine-containing phage carrying that gene(s). The required protein would then have to be directed by the cytosine-containing DNA: it is looked for directly on polyacrylamide gels or through its physiological effects or both. For all early proteins examined in this way, no synthesis was observed when 95 to 100% of the hydroxymethylcytosine was substituted by cytosine in the infecting DNA, whereas there was significant synthesis with 75% substitution or less. The results indicate that gpalc is carried in with the infecting DNA or is made very early to block transcription of all cytosine-containing DNA.

Control of promoter utilization by bacteriophage T4-induced modification of RNA polymerase alpha subunit

After infection of Escherichia coli cells, bacteriophage T4 induces several changes in the host DNA-dependent RNA polymerase. A well-characterized chemical change is a two-step ADP-ribosylation of the enzyme's alpha subunit (1). In order to investigate the effect of this change on RNA polymerase transcriptional properties in an in vitro system, we have reconstituted the enzyme from separated individual subunits which were obtained from normal or T4-modified RNA polymerases. It is demonstrated that the enzymes containing T4-modified alpha differ from the enzymes with normal alpha in two respects: (i) their overall activity on T4 DNA is reduced and (ii) they fail to utilize certain T4 promotors while efficiently utilizing other promoters. Among the promoters which are switched off by alpha modification are the two promoters of the D region and one of the two promoters of the T4 tRNA gene cluster. The differential effect of alpha modification on the expression of the tRNA and the D regions in vitro correlates with the previously established pattern of their transcription in vivo. It is suggested that the T4-induced ADP-ribosylation of RNA polymerase alpha subunit is involved in the shutoff of the early bacteriophage genes at the late stage of phage development.

Changes in the promoter range of RNA polymerase resulting from bacteriophage T4-induced modification of core enzyme

Primary transcripts made in vitro on bacteriophage T4 DNA by RNA polymerase isolated from normal or T4-infected Escherichia coli were compared by gel electrophoresis. Bacteriophage-modified RNA polymerase fails to initiate transcription at certain promoters recognized by unmodified enzyme. In the T4tRNA gene region, only one of the two promoters is active with the modified RNA polymerase. Reconstitution of separated RNA polymerase components demonstrates that this change in promoter site selection results from the modification of core enzyme and not sigma factor.

DNA-RNA polymerase complexes associated with the membrane from bacteriophage T2- or T4-infected Escherichia coli. I. General properties

Properties of DNA-RNA polymerase complexes, apparently bound to a fraction of the cell membrane of bacteriophage T2- or T4-infected Escherichia coli, are described. Evidence is presented to show that the complexes initiate the asymmetric synthesis of RNA, and release the finished product. The transcription capacity per unit of beta' + beta was 10 times higher at 6 min than at 30 min after infection.

Distinctive protein requirements of replication-dependent and -uncoupled bacteriophage T4 late gene expression

This paper further explores the relationship of viral DNA replication to bacteriophage T4 late gene expression. It is shown that replication coupled and -independent late transcription make different qualitative or quantitative demands on phage protein synthesis. In further analysis of these different protein synthesis requirements, experiments were performed with a temperature-sensitive mutant in T4 gene 55 (ts553). It is known that the gene 55 product regulates T4 late gene expression and binds to RNA polymerase. In the experiments presented here, it is shown that the temperature sensitivity of the ts553 gene 55 protein depends on whether it is involved in replication-coupled or -independent T4 late transcription. This is evidence that the proteins constituting the transcription apparatus interact differently with late transcription units in T4 DNA, depending on whether late transcription is replication coupled or independent.

Effect of salt on the transcription of T7 DNA by RNA polymerase from T4 phage-infected E.coli

Transcription of T7 DNA by T4 core enzyme with host sigma is more sensitive to KCI than that by host core enzyme with host sigma. When salt is added after initiation of RNA chains has occurred, it is not inhibitory. Salt affects the binding of T4 enzyme to T7 DNA to the same degree as the binding of host enzyme. Active preinitiation complex formation is inhibited more by salt with the T4 enzyme and the inhibition is temperature-dependent.

Bacillus subtilis ribonucleic acid polymerase mutants conditionally temperature sensitive at various stages of sporulation

Rifampin-resistant mutants of Bacillus subtilis that are conditionally temperature sensitive during sporulation have been isolated and characterized. The mutants can grow at the same rate as the wild type at the nonpermissive temperature but cannot sporulate. Depending on the mutation, they are blocked at either stage 0 to I, II, II to III, or IV of sporulation. The mutants showed an altered pattern of RNA synthesis after the stage at which they were blocked. The effect of rifampin on the activity of enzymes from mutant vegetative cells and sporulating cells was significantly different, suggesting that the RNA polymerase from sporulating cells was different from the RNA polymerase of vegetative cells. These results suggest that the conformation of the RNA polymerase core plays an important role in determining correct transcription during sporulation.

Phage T4 infection restricts rRNA synthesis by E. coli RNA polymerase

RNA polymerase from T4 infected cells supplemented with E. coli sigma polypeptide has a lower affinity for rRNA promoters than RNA polymerase from uninfected cells. The pattern of transcription by the phage modified polymerase is qualitatively similar to that of the vegetative polymerase in the presence of ppGpp. We suggest that E. coli polymerase holoenzyme normally exists in at least two conformational states, one with a high affinity for rRNA promoters and another with a low affinity, and that T4 infection stabilises the low affinity form.

DNA strand specificity of temporal RNA classes produced during infection of Bacillus subtilis by SP82

The DNA of the Bacillus subtilis bacteriophage SP82 has been separated into heavy (H) and light (L) fractions by centrifugation in buoyant density gradients in the presence of polyguanylic acid. Competition-hybridization experiments were performed with these separated fractions using RNAs isolated from cells labeled at intervals which account for 80% of the lytic cycle and unlabeled competitor RNAs isolated from phage-infected cells at 2-min intervals throughout infection. The analysis of temporal RNA classes were facilitated by use of a double reciprocal plot of the data. Five temporal classes binding to the H fraction and three binding to the L fraction were detected; the possible existence of an additional class transcribed from the H fraction is discussed. RNA synthesized in the presence of chloramphenicol contains two of the three classes produced from L-DNA and two of the five classes transcribed from H-DNA.

Evolution of the transcription complex during sporulation of Bacillus subtilis

Ribonucleic acid polymerase activity in partially purified extract of cells of Bacillus subtilis harvested at different times (t-1, to, t1, and t2) was studied by zone centrifugation. During the course of sporulation, vegetative sigma-factor activity decreased and the transcription complex lost some of its affinity for active sigma factor. The complex underwent a two-stage change in sedimentation value, from 14.5S in vegetative growth phase to a 13S species very early in sporulation to a 16S species at later times. Two SpoO mutants have been studied by zone centrifugation. One strain, a rifampin-resistant (RfmR) mutant, failed to show any modification of the transcription complex, whereas the other, a Rfms strain, underwent a partial evolution of the transcription complex after to.

Characterization of an inhibitor causing potassium chloride sensitivity of an RNA polymerase from T4 phage-infected Escherichia coli

The nature of the inhibition by salt (KCl) of DNA-dependent RNA polymerase from T4 phage-infected Escherichia coli (T4 enzyme) was studied using holoenzyme preparations, core enzyme and sigma fractions obtained by phosphocellulose column chromatography, and sigma fractions further purified by gradient centrifugation in the presence and absence of 6 M urea. We showed with holoenzyme preparations that salt inhibits the formation of rifampicin-resistant preinitiation complexes. The inhibition was considerably reduced when a nonionic detergent (particularly of the Triton series) was included in the reaction mixtures. With T4 core enzyme and T4 sigma fractions together with the same fractions from uninfected cells (host enzyme fractions) and different DNA templates, we showed that the T4 sigma fraction plays a role in the salt-sensitive activity with T4 DNA. The salt sensitivity of the T4 sigma fraction was antagonized by Triton; it was not a function of sigma fractions isolated from phage cultures infected in the presence of chloramphenicol. As reported previously (Stevens, A. (1973), Biochem. Biophys. Res. Commun. 54, 488), the T4 sigma fraction inhibited the activity of host sigma when they were present together in reaction mixtures, particularly in the presence of salt. T4 sigma further purified by centrifugation in glycerol gradients had the same properties as the cruder fraction, and the T4-specific polypeptide of mol wt 10000 (Stevens, A. (1972), Proc. Natl. Acad. Sci. U.S.A. 69, 603) was found in the same fractions. If the glycerol gradients contained 6 M urea, the mol wt 10000 polypeptide was separated from the salt-stimulated sigma. Fractions containing the small polypeptide could be added back to produce the salt-inhibitory effects. The inhibitory activity of both the crude sigma fraction and the fractions containing the small polypeptide was inactivated at 65 degrees C. The results suggest that the mol wt 10000 protein is a salt-promoted inhibitor, but the small amounts of it which are present in purified fractions of the T4 enzyme have not yet allowed its isolation in large enough quantities to permit a detailed study of its properties.

Bacteriophages of Bacillus subtilis

Images

Characterization of new regulatory mutants of bacteriophage T4. II. New class of mutants

New mutants of bacteriophage T4 that overproduce the enzyme dihydrofolate reductase were investigated. Unlike previously described overproducers of this enzyme (Johnson and Hall, 1974), these mutants did not overproduce deoxycytidylate deaminase. Overproduction of dihydrofolate reductase by the new mutants occurred because enzymatic activity continued to increase for a longer period of time in cells infected by the mutants than in cells infected by wild-type phage. This continued increase occurred even in the presence of rifampin, indicating that the overproduction is probably due to a post-transcriptional event. Both these new overproducers and the previously described overproducers were studied by using polyacrylamide gel electrophoresis. The two types of overproducers appeared to be very different. The previously described overproducers showed a delay and/or reduction in the synthesis of several proteins that normally started to be made 4 to 6 min after infection. Several proteins could be seen to be overproduced on the gels. The new overproducers did not show the delay in the synthesis of some proteins and only overproduced a few proteins. The new gene defined by the new overproducers is between the gene coding for thymidine kinase and the gene coding for lysozyme.

Purification and properties of a bacteriophage T5-modified form of Escherichia coli RNA polymerase

A modified form of Escherichia coli RNA polymerase that contains one of the three T5-specific polypeptides known to interact with the host enzyme was purified from bacteriophage T5-infected cells. The properties of this T5-modified enzyme appeared identical to those of the RNA polymerase derived from uninfected non-colicinogenic cells and to a fully active enzyme isolated from T5-infected ColIb+ cells after the limited in vivo transcription of T5 genes allowed by the plasmid had ceased.

The regulation of transcription in bacteriophage T5-infected Escherichia coli

The expression of bacteriophage T5-specific RNA and protein in infected cells is temporally separated into three classes: class I (preearly), class II (early), and class III (late). By immunoprecipitation techniques we have shown that T5 infection of cells leads to the synthesis of one class I polypeptide (11,000 daltons) and two class II polypeptides (90,000 and 15,000 daltons) capable of binding to the RNA polymerase of the host Escherichia coli cell. One of the class II polypeptides (90,000 daltons) is the product of gene C2, which is an essential gene product required for the initiation of class III RNA synthesis. The colicinogenic factor, ColIb, is a plasmid which prevents the normal synthesis of class II and the III bacteriophage T5-specific RNA in infected colicinogenic (ColIb+) cells. In T5-infected colicinogenic cells, only the T5 class I polypeptide is found associated with the RNA polymerase. Mutants of T5, designated T5h minus, are capable of growth on both noncolicinogenic and ColIb+ hosts. Extracts of T5h minus infected ColIb+ cells were shown to lack a small class I polypeptide (12,000 daltons) as compared to T5-infected cells. The h minus mutation, however, has no effect on the levels of the class I T5 polypeptide of similar molecular weight which is bound to the RNA polymerase. One effect of the h minus mutation is to enhance the quantities of the two class II polypeptides bound to the enzyme.

New phage-SPO1-induced polypeptides associated with Bacillus subtilis RNA polymerase

RNA polymerase was precipitated from extracts of Bacillus subtilis infected with phage SP01 by antiserum prepared against core RNA polymerase. As shown by sodium dodecyl sulfate gel electrophoresis, the precipitates contained at least five new polypeptides not present in uninfected bacteria, in addition to the known subunits of RNA polymerase. The molecular weights of these polypeptides are (1) 85,000; (II) 40,000; (III) 28,000; (IV) 25,000; and (V) 23,000. Four of the polypeptides (I, III, IV, and V) co-purified with RNA polymerase through gel filtration and phosphocellulose chromatography. A pulse-chase experiment indicated that all five polypeptides are synthesized de novo after infection. The synthesis of polypeptides II, III, and IV commences almost immediately after infection, while polypeptides I and V first appear several minutes later. A sus mutant blocked early in transcription, susF21 [Fujita, et al. (1971) J. Mol. Biol. 57, 301-317] failed to induce polypeptides I, IV, and V, while two other mutants, susF4 and susF14, blocked late in transcription both failed only to induce polypeptide V.

An immunological assay for the sigma subunit of RNA polymerase in extracts of vegetative and sporulating Bacillus subtilis

The activity of the sigma subunit of Bacillus subtilis RNA polymerase decreases markedly during the first hours of sporulation [T.G. Linn et al. (1973) Proc. Nat. Acad. Sci. USA 70, 1865-1869]. We have prepared antibody against RNA polymerase holoenzyme to determine the fate of sigma polypeptide during spore formation. This antiserum specifically and independently precipitates sigma and core polymerase from crude extracts of B. subtilis as judged by both sodium dodecyl sulfate and urea gel electrophoresis of the precipitates. We report that crude extracts of sporulating cells lacking sigma activity contain as much sigma polypeptide as extracts of vegetative cells. However, sigma polypeptide in extracts from sporulating cells is apparently only weakly associated with RNA polymerase, as indicated by the failure of sigma to co-purify efficiently with core enzyme during phase partitioning. The loss of sigma activity and the weak binding of sigma to core enzyme occurs normally in a mutant blocked at an intermediate stage of sporulation (SpoII-4Z) and in wild-type bacteria sporulating in 121B medium, Difco sporulation medium, or Sterlini-Mandelstam resuspension medium. In contrast, sigma in two mutants (SpoOa-5NA and SpoOb-6Z) blocked at an early stage of spore formation remains active and tightly associated with RNA polymerase during stationary phase.