Interaction of the sigma factor and the nusA gene protein of E. coli with RNA polymerase in the initiation-termination cycle of transcription

Sequences required for antitermination by phage 82 Q protein

The gene Q antiterminator proteins of phages lambda and 82 modify RNA polymerase at sites (named qut) that are close to, and apparently inseparable from the promoters themselves. Modification occurs while RNA polymerase has paused close to the start site, at nucleotide 16 for lambda, and nucleotides 15 and 25 for phage 82. We present a deletion analysis of the phage 82 qut site that identifies sequences required for pausing and shows that these sequences also are required for efficient Q function in vivo and in vitro. We show (1) that deletions as close as +5 to the RNA start site retain some ability to be modified by Q82, suggesting that part of the qut site is in the non-transcribed region of the promoter; (2) that NusA protein is required for activity of Q82 on certain qut82 site deletions, whereas it only modestly stimulates antitermination from the native qut82 site; and (3) that qut82 is active only on RNA polymerase that initiates at the qut-associated promoter, and not on RNA polymerase that initiates upstream and passes through an otherwise active qut82 site.

Murine monoclonal antibodies which recognize active sites of Escherichia coli NusA protein and epitope mapping by gene fusion

Seven hybridomas producing murine monoclonal antibodies reactive against NusA protein of Escherichia coli were prepared. Antigenic determinants of these monoclonal antibodies have been mapped by immunoblotting analyses using fusion proteins containing parts of NusA. The epitope of the N14 antibody maps in a hydrophobic amino acid (aa) cluster and consists of at least Ala-181 and Ser-183 residues. nusA1 and nusA11 mutations, which cause aa changes of these residues, abolish the antigenic reactivity to the N14 antibody. These antibodies react with intact NusA protein, indicating that the epitopes are exposed on the surface of NusA. Most of these epitopes cluster around the nusA1 and nusA11 mutation loci.

Dynamic interaction between a Drosophila transcription factor and RNA polymerase II

We have purified factor 5, a Drosophila RNA polymerase II transcription factor. Factor 5 was found to be required for accurate initiation of transcription from specific promoters and also had a dramatic effect on the elongation properties of RNA polymerase II. Kinetic studies suggested that factor 5 stimulates the elongation rate of RNA polymerase II on a dC-tailed, double-stranded template by reducing the time spent at the numerous pause sites encountered by the polymerase. The factor was found to be composed of two polypeptides (34 and 86 kilodaltons). Both subunits bound tightly to pure RNA polymerase II but were not bound to polymerase in elongation complexes. Our results suggest that factor 5 interacts briefly with the paused polymerase molecules and catalyzes a conformational change in them such that they adopt an elongation-competent conformation.

Overexpression of N antitermination proteins of bacteriophages lambda, 21, and P22: loss of N protein specificity

The N protein of bacteriophage lambda (N lambda) modifies Escherichia coli RNA polymerase in such a way that it transcribes through termination signals, a process called antitermination. N antitermination normally occurs only if the template contains a specific utilization or nut site upstream of the terminators and only in the presence of host-encoded Nus proteins. The lambda-related phages 21 and P22 produce N analogs, N21 and N22, but these require different nut sites and show a different pattern of functional interaction with one of the Nus factors, NusA, according to whether this protein is of E. coli or Salmonella origin (NusAEc or NusASal). We report the overproduction of N lambda, N21, or N22, each of which was induced by isopropyl-beta-D-thiogalactopyranoside at 37 degrees C from its cloned position downstream from ptac on a high-expression plasmid, each in a host that provided NusAEc or NusASal. Overproduction of each of these N proteins resulted in relaxed specificity for nut, which was shown by the ability to complement N mutants of heterologous phages; NusA specificity was determined by the N type that was present in these complementation tests. We also observed that excess N was able to suppress transcriptional polarity in the particular case of cloned 'trpA, the last gene of the tryptophan operon, although there was no effect on polarity within chromosomal trpE. Such polarity is attributed to the presence of cryptic intragenic terminators that become exposed in the absence of translation. Because there is no known nut site cis to 'trpA, we suggest that the 'trpA segment itself fortuitously contains a nut sequence that is able to function with excess N of any of the types tested and with either NusAEc or NusASal. We also found that excess N of any specificity, or even inactive N with missense mutation, could cause an increase in the level of NusAEc or NusASal, possibly because interaction between N and NusA, but independent of nut, whether functional or not, interferes with the autoregulation of NusA synthesis. These observations highlight the importance of protein concentration for the specificity of interactions both with other proteins and with nucleic acids. They also indicate that the interaction between N and NusA requires nut participation both for specificity and functionality.

Dynamic interaction between a Drosophila transcription factor and RNA polymerase II

We have purified factor 5, a Drosophila RNA polymerase II transcription factor. Factor 5 was found to be required for accurate initiation of transcription from specific promoters and also had a dramatic effect on the elongation properties of RNA polymerase II. Kinetic studies suggested that factor 5 stimulates the elongation rate of RNA polymerase II on a dC-tailed, double-stranded template by reducing the time spent at the numerous pause sites encountered by the polymerase. The factor was found to be composed of two polypeptides (34 and 86 kilodaltons). Both subunits bound tightly to pure RNA polymerase II but were not bound to polymerase in elongation complexes. Our results suggest that factor 5 interacts briefly with the paused polymerase molecules and catalyzes a conformational change in them such that they adopt an elongation-competent conformation.

Three rpoBC mutations that suppress the termination defects of rho mutants also affect the functions of nusA mutants

We have mapped three Escherichia coli RNA polymerase mutations selected by Guarente (1979) to suppress the termination defects of rho201. We find that two of the mutations are located in the 3' half of the rpoB gene encoding the beta subunit. The third mutation is in the rpoC gene, encoding the beta' subunit. All three RNA polymerase mutations affect termination efficiency, even in rho+ strains, suggesting that the C-terminal end of the beta as well as the beta' subunit participates in termination. In addition we find that all three rpoBC alleles inhibit lambda N-mediated antitermination at 30 degrees C in a strain containing the nusA1 allele. It may be significant that the three other RNA polymerase mutations known to revert the termination defect of mutant rho alleles also affect N-mediated antitermination in nusA1 strains. The correlation of these two phenotypes suggests that both phenotypes may arise from the same functional defect in RNA polymerase.

Effects of rifampicin resistant rpoB mutations on antitermination and interaction with nusA in Escherichia coli

Rifampicin resistant (Rifr mutations map in the rpoB gene encoding the beta subunit of Escherichia coli RNA polymerase. We have used our collection of 17 sequenced Rifr mutations to investigate the involvement of E. coli RNA polymerase in the antitermination systems enhancing expression of delayed early lambda genes or stable RNA. We have found that Rifr mutations affect both lambda N-mediated antitermination and the cellular antitermination system involved in synthesis of stable RNA. Because NusA is involved in antitermination and termination, we also investigated the interaction of NusA and RNA polymerase by determining whether Rifr mutations alter NusA-dependent termination or antitermination in cells with defective nusA alleles. We have shown that Rifr mutations can either enhance or suppress the phenotypes of defective nusA alleles. Most Rifr mutations alter the temperature range over which the nusA1 allele supports lambda N-mediated antitermination. In addition, a number of Rifr alleles restore termination to the nusA10(Cs) and the nusA11(Ts) mutants defective in this process. Our results indicate that the region of the rpoB gene defined by the Rifr mutations is involved in the antitermination process and affects the activity of the NusA protein directly or indirectly.

Regulation of DNA superhelicity by rpoB mutations that suppress defective Rho-mediated transcription termination in Escherichia coli

The highly defective rho-15 mutant of Escherichia coli produces plasmid DNA that is 22% less negatively supercoiled than DNA from an isogenic wild-type strain (J. S. Fassler, G. F. Arnold, and I. Tessman, Mol. Gen. Genet. 204:424-429, 1986). We extended our measurements of plasmid superhelicity to additional rho mutants and to strains containing mutations that suppress rho transcription termination defects; the suppressor mutations were in the rpoB and the rho genes. The superhelicity of plasmid DNA was reduced by 11 and 10%, respectively, in the rho-702 and rho-201 mutants, both of which are less defective in Rho-mediated transcription termination than rho-15. Plasmid superhelicity was restored in all the suppressed rho mutants; in one rpoB mutant, plasmid DNA was even more negatively supercoiled than in rpoB+ cells, whether in a rho+ or rho mutant background. Suppression of rho mutants enabled them to maintain plasmids that could not be maintained in the mutants in the absence of the suppressor mutations. The results indicate that in addition to DNA gyrase, topoisomerase I, and Rho, RNA polymerase is also a determinant of DNA superhelicity, and its effect is modified by the Rho protein. We propose that Rho may increase the degree of DNA unwinding by the transcription complex, possibly at transcription termination sites.

Nus A protein affects transcriptional pausing and termination in vitro by binding to different sites on the transcription complex

We examined the in vitro concentration dependence of the effects of Nus A on transcription termination and pausing to determine if Nus A affects both pausing and termination in vitro by binding to a single site on the transcription complex. Nus A was shown to cause maximal increases of pausing at a concentration approximately equimolar to RNA polymerase. However, the effects of Nus A on termination require much higher Nus A concentrations than are required for pausing. It is therefore likely that the effects of Nus A on pausing and termination result from the binding of Nus A to different sites on the transcription complex. Since proteins that probably bind RNA nonspecifically were also shown to strongly reduce termination at a Rho-dependent terminator, Nus A may decrease Rho-dependent termination by binding nonspecifically to RNA. This proposal is consistent with most of the available data on the in vitro effects of Nus A and provides a mechanistic basis for previously unexplained details of Nus A caused decreases in Rho-dependent termination. We further speculate that most or all of the in vivo roles of Nus A may involve the enhancement of pausing.

Effects of Escherichia coli Nus A protein on transcription termination in vitro are not increased or decreased by DNA sequences sufficient for antitermination in vivo

The ability of Escherichia coli Nus A protein to recognize specific DNA or RNA sequences in vitro was tested by using transcription templates containing a variety of promoters, transcription terminators, and antitermination-conferring regions. We conclude that the effects of Nus A on termination are not qualitatively or quantitatively altered by sequences present in promoters, Rho-dependent terminators, or antitermination-conferring regions. Nus A was also shown to increase termination at the rrnC Rho-independent T1 terminator by a mechanism that is independent of the promoter or sequences involved in antitermination. Altogether, these observations argue against a direct Nus A-nucleic acid interaction affecting termination in vitro. Together with the results described in the accompanying paper [Sigmund, C. D., & Morgan, E. A. (1988) Biochemistry (preceding paper in this issue)], these results suggest that the effects of Nus A on termination in vitro may not be related to the in vivo functions of Nus A.

Transcription termination in Escherichia coli. Measurement of the rate of enzyme release from Rho-independent terminators

The termination/release phase of transcription must involve at least three major steps: cessation of elongation; release of the transcript; and release of the RNA polymerase. We have devised a novel method for measuring the rate of Escherichia coli RNA polymerase release during transcription termination. The method is based on a kinetic analysis of the rate of RNA synthesis during steady-state transcription. Using this method with defined transcription units, we have found that RNA polymerase release occurs rapidly from several rho-independent terminators. Enzyme release from the T7 early terminator occurs within 13(+/- 3) seconds of the cessation of elongation. Neither nusA protein nor supercoiling of the DNA template affects the rate of enzyme release. However, addition of excess sigma factor significantly increases the rate of enzyme recycling during the steady state. Since added sigma factor does not alter the rates of initiation and elongation by E. coli RNA polymerase holoenzyme, it appears that sigma factor stimulates one or more steps in the termination/release process and reduces the rate of enzyme release to a few seconds. We present evidence that suggests sigma may be directly involved in catalyzing release of the core RNA polymerase from the DNA template during transcription termination. The rapid rates of enzyme release we measure make it difficult to be certain of the exact pathway of events that occur in the termination/release phase of transcription. The most plausible pathway involves initial release of the RNA transcript followed by release of core RNA polymerase from the DNA. Studies on the properties of core polymerase-RNA complexes indicate that core polymerase and the RNA transcript probably do not dissociate as a complex from the terminator. Furthermore, these core-RNA complexes are too stable to represent significant intermediates in the termination/release pathway, at least in the early steps of the reaction.

NusA protein is necessary and sufficient in vitro for phage lambda N gene product to suppress a rho-independent terminator placed downstream of nutL

Transcription antitermination by phage lambda N protein is reproduced in vitro solely with purified components. We have placed a strong rho-independent terminator, lambda tR', in the PL operon about 200 base pairs downstream from the N-recognition site, nutL, and have monitored terminated and run-off transcripts produced by single-round transcription of linear plasmids. In the presence of NusA, one of several host factors implicated in antitermination, N is found to virtually abolish termination at tR'. N is unable to suppress termination if the terminator is preceded by a defective nut site. Thus, during transcription through the nut site, N and NusA can modify RNA polymerase to a termination-resistant form in the absence of any other accessory factor.

An elongation control particle containing the N gene transcriptional antitermination protein of bacteriophage lambda

The N gene transcriptional antitermination protein of bacteriophage lambda is incorporated in vitro into transcriptional elongation complexes containing the E. coli proteins NusA and NusB. The binding of NusA to elongating RNA polymerase is sequence-independent and follows the release of sigma 70. Incorporation of N into the elongation complex requires an N utilization site (nut site) on the DNA template. Incorporation of NusB into the complex requires NusA, ribosomal protein S10, and the boxA component of the nut site. T1 RNAase releases N, but not NusB, from the elongation complex. We therefore propose that an N-modified termination-resistant elongation complex includes an elongation control particle (ECP) containing at least NusA, NusB, S10, N, and an RNA transcript of the nut site.

The remarkable specificity of a new transcription termination factor suggests that the mechanisms of termination and antitermination are similar

E. coli lysogenic for the temperate, lambda-related phage HK022 do not support lambda growth. The exclusion of lambda is caused by the HK022 nun gene product, which blocks the expression of genes located downstream of and in the same transcription unit as the lambda nutL and nutR sequences. Transcripts terminating prematurely at or near nutR have been detected after inactivation of lambda repressor in lambda, HK022 dilysogens. Nun therefore appears to be a transcription termination factor with a remarkable specificity; it converts the lambda nut sequences, which normally interact with lambda N protein to suppress transcription termination, into terminators. These and other similarities between Nun-promoted termination and N-promoted antitermination argue strongly that the mechanisms of the two reactions have steps in common.

An antitermination protein engages the elongating transcription apparatus at a promoter-proximal recognition site

As a transcriptional activator, the N protein of phage lambda acts to suppress transcription termination by recognizing a promoter-proximal site, nut, which is separated from the terminators by thousands of base pairs. We demonstrate here that N interacts with the elongating RNA polymerase in transit through the boxB domain of nut. This interaction leads to the stable association of N as an integral component of the transcription apparatus. During subsequent elongation, N translocates along with polymerase through several defined terminators positioned beyond nut. Therefore, by being an operon-specific subunit of the transcription apparatus, N presumably prevents the interaction of polymerase with termination signals.

Isolation and structural analysis of the Escherichia coli trp leader paused transcription complex

Transcription pausing is a key step in many prokaryotic transcription attenuation mechanisms. Pausing is thought to occur when an RNA hairpin forms near the 3' end of a growing transcript. We report here the isolation of the trp leader paused transcription complex containing a defined 92-nucleotide nascent transcript. Digestion of isolated paused complexes with RNase T1 suggests that the trp leader RNA hairpin designated 1:2 forms in the paused transcription complex. The transcription factor NusA alters the RNase T1 digestion pattern of the 92-nucleotide pause transcript in the complex but not the cleavage patterns of purified pause RNA, suggesting that NusA specifically affects the 1:2 hairpin in the paused transcription complex. The isolated paused transcription complex retains the ability to resume transcription. Kinetic studies on the resumption of elongation suggest that NusA is a non-competitive inhibitor of paused complex release and that the Ks for GTP is around 300 microM. RNA polymerase in the paused transcription complex protects approximately 30 base-pairs on both DNA strands from exonuclease digestion.

Identification of intrinsic termination sites in vitro for RNA polymerase II within eukaryotic gene sequences

We have identified and mapped several DNA sequences within a human histone gene (H3.3) at which in-vitro transcription by highly purified RNA polymerase II is efficiently terminated. Since transcription in our system involves only RNA polymerase II acting on a linear DNA template, these sequences contain "intrinsic" termination signals recognized by the polymerase protein itself. The existence of such signals within a gene suggests that efficient antitermination systems probably exist for mammalian transcription units. Alternatively, there could be a high frequency of premature transcription termination, or "polarity" for genes such as H3.3. Intrinsic transcription termination sites in H3.3 are located in sequences of consecutive thymidylate residues (5 to 8 nucleotides) on the non-transcribed DNA strand (T-runs), from which it is likely that such T-runs are elements of the intrinsic termination signal for RNA polymerase II. However, transcription proceeds without significant termination through many similar T-runs, from which it follows that these intrinsic termination signals include other elements. Since transcription is also terminated efficiently at these sites when the transcript remains bound along its full length as a DNA-RNA hybrid, it is unlikely that formation of specific RNA secondary structures in the transcript is a general element of the intrinsic termination signal. Although DNA sequences downstream from the coding portion of the mouse beta-globin gene have been implicated as sites of transcription termination in vivo, these regions do not contain strong intrinsic termination signals, and transcription in vitro proceeds through these regions almost undiminished. Transcriptional termination in this region in vivo may depend on the presence of termination factors or other intracellular elements, and there may be multiple classes of DNA signals that control eukaryotic termination.

Mapping and characterization of transcriptional pause sites in the early genetic region of bacteriophage T7

During transcription of DNA templates in vitro, Escherichia coli RNA polymerase pauses at certain sequences before resuming elongation. Previous studies have established that some pausing events are brought about by the formation of RNA hairpin structures in the nascent transcript; however, it is not known whether this is an invariant and causal relationship. We have mapped and characterized almost 200 distinct pause sites located within the early region of bacteriophage T7 DNA using a collection of T7 deletion mutant DNAs and taking advantage of a procedure that permits synchronous transcription from the T7 A1 promoter. The pausing pattern is sensitive both to the overall concentration of nucleotide substrates and to the relative concentrations of the four nucleotides. The apparent Ks value for a particular nucleoside triphosphate can vary over a 500-fold range depending on the nucleotide sequence, and pausing at some sites can be induced by modest reductions in substrate concentrations. However, pausing is not solely a consequence of substrate limitation. Pausing at certain sites is caused by some feature of the template or of the transcript itself. Substitution of inosine triphosphate (ITP) for GTP during transcription strongly affects the pattern and strength of pausing events, suggesting that base-pairing interactions involving the RNA strand are important for some pausing events. Other pauses are determined by sequences downstream from the elongation site that have not yet been transcribed, and pausing at these sites is generally insensitive to substitution of IMP for GMP in the nascent transcript. Pausing at one particular site on T7 DNA is strongly enhanced by the presence of E. coli gene nusA protein. These results confirm that there are multiple classes of sites that lead to transcriptional pausing, and provide a collection of sites for further study. Using selected pause sites in the early region of T7 DNA, we have tried to evaluate the possible roles of primary sequence, base composition and secondary structure in pausing. Computer analysis was used to compare primary sequences and potential RNA hairpin structures in transcripts for pauses known to share similar biochemical properties. We see no correlation of pause sites with regions of particular base composition or with specific primary sequences. While some pauses are correlated with the potential to form stable RNA hairpins just upstream from the growing point of the RNA chain, there is not a strict one-to-one relationship between predicted RNA hairpins and the location of pause sites.(ABSTRACT TRUNCATED AT 400 WORDS)

nusA protein of Escherichia coli is an efficient transcription termination factor for certain terminator sites

We have studied the factors that affect transcription termination in vitro at the tR2 terminator of bacteriophage lambda and at the T1 terminator of the Escherichia coli rrnB operon. Termination efficiency at both of these sites is enhanced by the E. coli nusA protein, giving final efficiencies of termination in vitro comparable to those estimated in vivo. Transcripts terminated in the presence of nusA protein are all released from the RNA polymerase complex, indicating that a complete termination reaction is involved, rather than simply induction of a long pause at the terminator. The termination factor activity of the nusA protein does not depend on the presence of rho protein and is not detectably enhanced by that factor. Thus, the nusA protein appears to play a pleiotropic role in E. coli transcription, serving as an antitermination factor, RNA polymerase subunit and true termination factor for some terminator sites.

Optimization of gene expression in Streptomyces lividans by a transcription terminator

The ability of an inverted repeat sequence (IRS) from the 3' end of the aph gene from Streptomyces fradiae to induce transcription termination in vivo has been examined. As a model system, a DNA fragment encoding the human interferon alpha 2 inserted in the Streptomyces plasmid pIJ702 was used. When the IRS was inserted downstream from this sequence and transcription assayed in Streptomyces lividans, highly efficient (approximately 90%) transcription termination was observed occurring immediately after the 3' terminus of the dyad. In contrast, gene constructions lacking the IRS transcribed longer mRNAs. Moreover, the IRS gave rise to increased amounts of the hIFN alpha 2 suggesting that the putative stem-loop structure stabilised the transcript.

The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon

The Pseudomonas putida TOL plasmid pWWO carries an operon that specifies a meta-cleavage pathway for the catabolism of benzoate and toluates whose transcription is positively regulated by the xylS gene product. Stimulation of transcription of the operon is thought to result from activation of this protein by pathway substrates/effectors. In the present study, overexpression of the xylS gene has led to identification of the regulator as a 33 kDa protein. Overexpression of xylS also resulted in partially constitutive, i.e. effector-independent expression of the meta-cleavage operon. Determination of the polynucleotide sequence of the xylS gene revealed amino acid sequence homology with several DNA binding proteins, particularly with the araC products of Escherichia coli and Salmonella typhimurium and with the nifA and ntrC products of Klebsiella pneumoniae. Homologous sequences were mainly located in an alpha-helix-turn-alpha-helix domain of the polypeptide. Interestingly, amino acid sequence homology was also found with sigma factors of E. coli (ntrA and htpR products) and Bacillus subtilis (spoIIG and phage SPOI Gp34 products) and other RNA polymerase core-interacting proteins, such as the E. coli nusA product.

Evidence that Rho and NusA are involved in termination in the rplL-rpoB intercistronic region

The frequency of transcription of the ribosomal protein and RNA polymerase gene segments of the rplKAJL-rpoBC gene cluster was measured for Escherichia coli K-12 strains carrying mutations in the genes for transcriptional termination factors. The results of our study suggest that Rho increases and that both NusA and the product of sfrB decrease termination frequency in the rplL-rpoB intercistronic region.

lambda N antitermination system: functional analysis of phage interactions with the host NusA protein

Coliphage lambda gene expression is regulated temporally by systems of termination and antitermination of transcription. The lambda-encoded N protein (pN) acting with host factors (Nus) at sites (nut) located downstream from early promoters is the first of these systems to operate during phage development. We report observations on some of the components of this complex system that, in part, address the way in which these elements interact to render RNA polymerase termination-resistant. (1) The isolation of a conditionally lethal cold-sensitive nusA mutation demonstrates that NusA is essential for bacterial growth. (2) The effect on lambda growth in a host in which the Salmonella NusA protein is overproduced suggests that NusA is essential for N-mediated antitermination in phage lambda. (3) A truncated NusA product, representing only the amino two-thirds of the native protein, is active for both bacterial growth and pN action, indicating that the carboxy end of the molecule may not be a functionally important region. (4) lambda pN can function with the heterologous nut region from Salmonella typhimurium phage P22 when lambda pN is overproduced, demonstrating that lambda pN can function with the nut regions of other lambdoid phages. (5) A single base-pair change in the lambda nutR boxA sequence that was selected to permit a lambda derivative to utilize the Salmonella NusA protein restores lambda growth in the Escherichia coli nusA1 host.

T-antigen-DNA polymerase alpha complex implicated in simian virus 40 DNA replication

We have combined in vitro DNA replication reactions and immunological techniques to analyze biochemical interactions between simian virus (SV40) large T antigen and components of the cellular replication apparatus. First, in vitro SV40 DNA replication was characterized with specific origin mutants. Next, monoclonal antibodies were used to demonstrate that a specific domain of T antigen formed a complex with cellular DNA polymerase alpha. Several antibodies were identified that coprecipitated T antigen and DNA polymerase alpha, while others were found to selectively prevent this interaction and concomitantly inhibit DNA replication. DNA polymerase alpha also bound efficiently to a T-antigen affinity column, confirming the immunoprecipitation results and providing a useful method for purification of the complete protein complex. Taken together, these results suggest that the T-antigen-polymerase association may be a key step in the initiation of SV40 DNA replication.

Multivalent regulation of the nusA operon of Escherichia coli

The rate of synthesis and intracellular content of the NusA protein, a transcription termination factor, were determined for wild-type and nusA and/or nusB mutants of Escherichia coli. Both the rate and content of NusA in wild-type strains were similar to that of the RNA polymerase sigma subunit, a transcription initiation factor, on a molar basis, and about 30%-40% the levels of RNA polymerase beta beta' subunits. At the stationary phase of cell growth, the values increased in parallel for both transcription factors up to approximately the level of the beta beta' subunits. In nus mutants, the rate of synthesis and the content of the sigma subunit were significantly increased. These observations together suggest that the two transcription factors are coordinately regulated.

Revised sequence of the nusA gene of Escherichia coli and identification of nusA11 (ts) and nusA1 mutations which cause changes in a hydrophobic amino acid cluster

The mutant nusA DNAs (nusA11 and nusA1) were sequenced. Single base substitutions caused by these mutations were found in the coding region of nusA. The nusA11 mutation, which is conditionally lethal, substituted Thr for the 181st Ala. Also, nusA1, which restricts lambda growth, substituted Ala for the 183rd Ser. These two positions were located in the same hydrophobic amino acid cluster. This cluster seemed to be an essential region in the functional domain of NusA. In the course of these experiments, several mistakes in the published nusA nucleotide sequence were found. These errors are revised in this article. The molecular weight of NusA is accordingly revised to 54,430.

T-antigen-DNA polymerase alpha complex implicated in simian virus 40 DNA replication

We have combined in vitro DNA replication reactions and immunological techniques to analyze biochemical interactions between simian virus (SV40) large T antigen and components of the cellular replication apparatus. First, in vitro SV40 DNA replication was characterized with specific origin mutants. Next, monoclonal antibodies were used to demonstrate that a specific domain of T antigen formed a complex with cellular DNA polymerase alpha. Several antibodies were identified that coprecipitated T antigen and DNA polymerase alpha, while others were found to selectively prevent this interaction and concomitantly inhibit DNA replication. DNA polymerase alpha also bound efficiently to a T-antigen affinity column, confirming the immunoprecipitation results and providing a useful method for purification of the complete protein complex. Taken together, these results suggest that the T-antigen-polymerase association may be a key step in the initiation of SV40 DNA replication.

The sigma subunit of RNA polymerase contacts the leading ends of transcripts 9-13 bases long on the lambda PR promoter but not on T7 A1

The sigma subunit of RNA polymerase is responsible for specific initiation of RNA synthesis at promoter sites on DNA. sigma dissociates shortly after initiation. Photoaffinity-labeling experiments performed on transcription complexes with two different DNA promoters, which have highly homologous control sequences upstream from the transcribed regions, have revealed that the sigma subunit of RNA polymerase is contacted by the 5' ends of quite different lengths of nascent RNA in each transcription complex. On the other hand, the labeling of subunits beta beta' is quite similar for both promoters, and the alpha subunit is not labeled in either case. The results of transcription experiments on the phage lambda PR promoter show that sigma can be photoaffinity labeled by RNA chains that are 9-13 nucleotides long and thus remains associated with the core enzyme at least to that point. But on the A1 promoter of phage T7 DNA, photoaffinity labeling of sigma ceases with the trinucleotide. Thus release of sigma from the vicinity of nascent RNA depends not merely on the length but on the sequence of the transcript. For the T7 A1 promoter, sigma labeling ceases while the leading end of the RNA is still base paired to the DNA template; thus, it appears that there is at least one site on the enzyme that interacts with the growing transcript/template hybrid, in a sequence-dependent way, to effect sigma release.(ABSTRACT TRUNCATED AT 250 WORDS)

Regulatory defects of a conditionally lethal nusAts mutant of Escherichia coli. Positive and negative modulator roles of NusA protein in vivo

Previous studies have attributed two activities to the NusA protein of Escherichia coli; namely, termination and antitermination of transcription. To examine these activities, we isolated a temperature-sensitive mutant of the nusA gene (nusAts11). The mutant cells produce a thermolabile NusA protein and grow at 32 degrees C, but not at 42 degrees C. At 42 degrees C, nusAts11 is recessive to nusA+ and nusA1, indicating the absence of its active gene product at that temperature. In the mutant, the efficiency of termination at the lambda tR1 terminator decreases, resulting in an increased expression of distal gene(s). On the other hand, the synthesis of the beta-galactosidase and beta beta' subunits of RNA polymerase is reduced in the mutant. This mimics effects seen in vitro when NusA protein is removed from a coupled transcription-translation system. These results suggest that the NusA protein plays both negative and positive modulator roles in vivo. The mutation nusAts11, unlike nusA1, does not block lambda phage growth at non-permissive temperatures, suggesting that NusA protein is not required for N antitermination in the mutant. Besides, the nusAts11 allows lambda Nam7Nam53byp phage growth under sup0 conditions, indicating that the N antitermination function is dispensable (at least partly) in this mutant.

Rho-dependent transcription termination in the tryptophanase operon leader region of Escherichia coli K-12

Recent studies have suggested that expression of the tryptophanase (tna) operon of Escherichia coli is subject to transcription termination-antitermination control (V. Stewart and C. Yanofsky, J. Bacteriol. 164:731-740, 1985). In vivo studies have indicated that the transcribed leader region, tnaL, contains a site or sites of rho-dependent transcription termination (rho is the polypeptide product of the gene rho). We now report direct in vitro evidence that tnaL contains rho-dependent termination sites. In vivo termination appeared to occur at the rho-dependent termination sites identified in vitro. Transcription pausing analyses correlated sites of pausing in tnaL with sites of rho-dependent termination.

The cloning and sequence of the gene encoding the omega subunit of Escherichia coli RNA polymerase

Omega is a small protein found associated with Escherichia coli RNA polymerase. The role of omega, if any, in transcription is not known. We have cloned the omega-encoding gene (rpoZ) so that we can produce large amounts of omega by over-production and to introduce mutations in its gene. We determined the N-terminal amino acid (aa) sequence of omega by aa microsequencing. Using the sequence we synthesized an eight-fold ambiguous 14-mer oligodeoxynucleotide probe and screened an E. coli genomic library using the base composition independent method of hybridization reported by Wood et al. [Proc. Natl. Acad. Sci. USA 82 (1985) 1585-1588]. With this method we isolated a clone that contained part of rpoZ which we used as a probe to isolate the complete gene. The sequence of the region containing the rpoZ gene predicts a highly charged protein of 91 aa with an Mr of 10 105. In addition, upstream from the gene is a good promoter-like sequence. We have verified by S1 mapping that in vivo transcripts originate from this promoter and possibly from a second promoter farther upstream.

Escherichia coli integration host factor inhibits the NusA stimulation of RNA polymerase sigma subunit synthesis in vitro

As reported previously, Integration Host Factor (IHF) stimulates cII expression but the stimulatory effect is prevented by the NusA protein (Peacock and Weissbach, 1985, Biochem. Biophys. Res. Commun. 127, 1026-1031). The interaction between IHF and the NusA protein has been investigated further in studies on the in vitro expression of the genes for the beta (rpoB) and sigma (rpoD) subunits of RNA polymerase, both known to be stimulated by NusA. The NusA stimulation of rpoD expression can be prevented by IHF, but IHF has no effect by itself on rpoD expression. IHF does not influence rpoB expression either in the presence or absence of NusA.

Cloning of the Escherichia coli gene for the stringent starvation protein

In order to clone the Escherichia coli gene for the stringent starvation protein (SSP), we determined its N-terminal sequence as well as the sequence of two peptide fragments obtained by cyanogen bromide cleavage of the protein. We then chemically synthesized four sets of oligodeoxyribonucleotide mixtures that represented possible codon combinations for parts of these amino acid sequences. The synthetic oligonucleotides were labelled with 32P at their 5'-termini and used as hybridization probes to detect DNA fragments containing the complementary sequences. Genomic Southern hybridization of E. coli chromosomal DNA gave up to ten DNA fragments hybridizing with each probe but only a few hybridized with two or more of the probes. The latter fragments were cloned in pBR322. By determining partial base sequences with a rapid method and examining proteins encoded by the DNA fragments, we were able to show that we had isolated a clone containing the complete SSP structural gene.

Efficient modification of E. coli RNA polymerase in vitro by the N gene transcription antitermination protein of bacteriophage lambda

The N gene protein of bacteriophage lambda prevents termination of transcription by E. coli RNA polymerase. We describe here the conditions of a cell-free reaction system in which pure N stimulates net transcription up to tenfold and therefore nearly stoichiometrically modifies transcribing RNA polymerase molecules. The reaction contains micrococcal nuclease-treated S100 extract derived from E. coli and a plasmid template DNA containing the lambda early promoter PL, the N utilization site nutL, and the Rho-dependent terminator tL1. Stimulation by N in this system is specific and biologically relevant since it is absent with vector pBR322 DNA and with extracts derived from E. coli strains bearing the nusA1 and nusE71 mutations known to block N function in vivo. We use the system to provide further evidence that ribosomes are not necessary for N function and to demonstrate the direct involvement in N function of the NusA protein of E. coli.

IHF stimulation of lambda cII gene expression is inhibited by the E. coli NusA protein

The effects of E. coli proteins Integrative Host Factor (IHF) and NusA on the regulation of lambda cII gene expression are presented. As reported previously (Peacock et al. [1984] Proc. Natl. Acad. Sci. USA 81, 6009-6013), IHF stimulates the DNA-directed in vitro synthesis of cII protein or its first dipeptide, fMet-Val. Whereas NusA, by itself, has no effect on cII expression, the presence of NusA inhibits the IHF-mediated stimulation of cII synthesis.

"N" transcription antitermination proteins of bacteriophages lambda, phi 21 and P22

Comparison is made among the amino acid sequences of three transcription antitermination proteins, based upon the DNA sequences of their genes in bacteriophages lambda, phi 21 and P22. The three proteins are all small (about 100 amino acids), hydrophilic and basic, but otherwise show little homology. A basic region near the amino terminus has several amino acid positions common to all three proteins and is the locus of mutations that alter six different amino acid positions inactivating the lambda N protein. A less basic region near the center is the locus of three mutations affecting the interaction of lambda N with host nusA protein. The N gene of phi 21 has an amino terminus more like that of P22, and a carboxy terminus clearly related to that of lambda.

Plasmid vectors designed for the analysis of transcription termination signals

We have constructed synthetic operons in which two genes (cat and lacZ or cat and galK) were placed in tandem under the control of the bacteriophage lambda oLpL operator and promoter. Restriction sites were introduced between the promoter and the proximal cat gene or between the cat and lacZ or galK genes. In the latter case, introduction of a transcriptional terminator between the two structural genes should affect only the distal gene. Thus, following induction, the expression of the cat gene serves as an internal control, compensating for changes due to plasmid copy number or possible decrease in transcription initiation. We used these plasmids to select a lambda DNA fragment which includes the N-unresponsive tJ transcriptional terminator. This DNA fragment was inserted between the cat and galK genes. Enzymatic assays of these two gene activities following induction indicate that transcripts initiated at the pL promoter under N+ conditions terminate at tJ between the two genes. S1-nuclease analysis showed that these transcripts terminate at several sites in the tJ region. Similar results were obtained whether the host cells were RNaseIII+ or RNaseIII-. As a control, we showed a complete antitermination of the lambda t'I terminator under similar conditions, indicating that a sufficient amount of the N gene product is made from one N gene copy to suppress terminators carried on multicopy plasmids.

In vitro stimulation of Escherichia coli RNA polymerase sigma subunit synthesis by NusA protein

A simplified DNA-directed in vitro system which measures synthesis of the NH2-terminal dipeptides of gene products has been used to study the expression of rpoD, the gene coding for the sigma subunit of Escherichia coli RNA polymerase. The rpoD gene is part of a complex operon which also includes the genes for ribosomal protein S21 (rpsU) and primase (dnaG). Primary promoters have been identified upstream of the structural genes, but there are secondary (internal) promoters within the dnaG gene that are involved in the expression of rpoD. Significant expression of the rpsU and rpoD genes was observed in the in vitro dipeptide system using plasmid pBS105, which contains both external and internal promoters. With plasmid pMRG-1, which contains only the internal promoters, only rpoD expression was observed. From either template, synthesis of the NH2-terminal dipeptide of sigma, fMet-Glu, is stimulated about threefold by the E. coli nusA gene product. In addition, NusA protein stimulates synthesis of the entire sigma protein in a defined in vitro system. NusA protein has no effect on the expression of the upstream gene rpsU, and the stimulation of rpoD expression by NusA protein is at the level of transcription. The results are consistent with the known role of NusA protein in modulating transcription at pause or attenuation sites.