Mapping and characterization of promoters in bacteriophages fd, f1 and m13

Escherichia coli RNA polymerase binding to a DNA terminus prevents formation of a closed promoter complex

A 302 bp DNA fragment and a 113 bp subfragment of the former, both containing the fd gene VIII promoter (P VIII), were found to exhibit temperature-dependent differential behaviour in RNA chain initiation from P VIII. At 37 degrees C no significant differences were observed, while at 17 degrees C chain initiation was strongly suppressed only with the 113 bp fragment. This phenomenon depended on the presence of the (blunt) DNA terminus upstream from P VIII (position -70). Footprinting revealed that at 17 degrees C RNA polymerase was bound to this DNA fragment in a different mode. Contacts were observed only upstream from position -25. On the contrary, at 37 degrees C only the promoter complex footprint was visible. These results indicate that at 17 degrees C formation of the non-initiating complex is more favourable than formation of the promoter complex (which is closed at 17 degrees C; Hofer, B., Müller, D. and Köster, H. (1985) Nucleic Acids Res. 13, 5995-6013) and that formation of both complexes is mutually exclusive. No footprints of RNA polymerase were observed at other DNA termini. This indicates a sequence-specificity for the interaction at the terminus of the 113 bp fragment. The footprint pattern, together with features of the DNA sequence, suggests that the contacts involved in this interaction are similar to those promoter contacts formed upstream from position -20 and that DNA without a -10 region can be specifically recognized by RNA polymerase.

A simple nonisotopic method for restriction mapping in single-stranded DNA cloning vectors based on taking timepoints during primed Klenow synthesis

A fast, simple, and nonisotopic method for restriction mapping inserts in single-stranded cloning vectors (such as M13 or single-stranded plasmids) is presented. The procedure uses a commercially available oligonucleotide sequencing primer to initiate Klenow-mediated, unidirectional DNA synthesis along the single-stranded insert DNA. Aliquots taken at very short timepoints from this reaction are quick-frozen, heat-inactivated, and restriction-digested with the restriction enzyme or enzymes of interest. When the samples are run on an agarose gel and stained with ethidium bromide, the restriction bands appear in the order of their proximity to the priming site. The method's advantages are that it is fast, unidirectional and thus relatively unambiguous, requires neither isotope nor elaborate DNA handling or extraction procedures, and resolves the ambiguities due to "near doublets" that often plaque double-digest mapping and partial-digest mapping. Tetranucleotide restriction maps extending up to 5 kb can be determined from a single priming experiment; more infrequent hexanucleotide restriction sites can be mapped over longer distances. Also, a single aliquot taken at an early timepoint can be restriction-digested to establish the orientation of cloned inserts.

Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps

The forward and reverse kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter have been studied in the temperature range of 15-42 degrees C. The standard two-step model, involving the formation of a closed intermediate, RPc, followed by an isomerization that leads to the active complex RPo, could not account for the present data. The promoter-enzyme lifetime measurements showed an inverse temperature dependence (apparent activation energy, -35 kcal/mol). A third step, which is very temperature dependent and which is very rapid at 37 degrees C, was postulated to involve the unstacking of DNA base pairs that immediately precedes open complex formation. Evidence for incorporating a new binary complex, RPi, in the pathway was provided by experiments that distinguished between stably bound species and active promoter after temperature-jump perturbations. These experiments allowed measurement of the rate of reequilibration between the stably bound species and determination of the corresponding equilibrium constant. They indicated that the third step became rate limiting below 20 degrees C; this prediction was checked by an analysis of the forward kinetics. A quantitative evaluation of the parameters involved in this three-step model is provided. Similar experiments were performed on a negatively supercoiled template: in this case the third equilibrium was driven toward formation of the open complex even at low temperature, and the corresponding step was not rate limiting.

The trfA and trfB promoter regions of broad host range plasmid RK2 share common potential regulatory sequences

The positions of the trfA and trfB promoters of broad host range IncP plasmid RK2 (identical to RP1, RP4, R68 and R18 ) were identified by RNA polymerase protection studies, and the nucleotide sequences of the promoter regions determined. A mutation within the trfA promoter sequence is associated with loss of kilD activity. In addition a probable promoter region for the kilB locus was identified. The three promoter regions share common palindromic sequences which may serve as sites for the coordinate regulation of replication and kil functions.

Major coat protein and single-stranded DNA-binding protein of filamentous virus Pf3

The region of the Pf3 virus genome encoding its major coat protein and its single-stranded DNA-binding protein is organized somewhat like the corresponding region of the fd (M13, f1) genome. Nevertheless, the major coat protein is unique among the major coat proteins of fd and the other filamentous phages studied in that it lacks a signal sequence and appears to be a direct translation product and in that it has fewer basic amino acid residues than its equivalent of DNA phosphates in the virion. These features are relevant to considerations of both protein insertion into membranes and DNA structure in filamentous viruses. The single-stranded DNA-binding protein also has a sequence that is different from the sequences of single-stranded DNA-binding proteins from other filamentous viruses.

A rho-dependent transcription termination signal in bacteriophage f1

The bacteriophage f1 intergenic region distal to gene IV encodes a rho-dependent transcription termination signal. Terminator function in vivo and in vitro is dependent upon active Escherichia coli rho protein, although the RNA 3' ends detected in vivo differ from those seen in vitro. The minimal sequence required for terminator function in a heterologous plasmid system encompasses approximately 100 nucleotides distal to gene IV, which can be drawn as a large hairpin structure. The in vivo rho-dependent 3' end occurs within this sequence, while the in vitro rho-dependent 3' ends occur just distal to it. In vivo in a rho mutant host, f1 transcripts pass through the rho-dependent sites and stop within a sequence of high potential secondary structure near the f1 origin of DNA replication. This sequence alone causes transcription termination in the heterologous plasmid system in vivo. In vitro in the absence of rho protein, transcription does not terminate within this sequence. The RNA 3' ends detected in these studies do not occur within A + T-rich sequences.

RNA polymerase from Rhizobium japonicum

DNA-dependent RNA polymerase (EC 2.7.7.6) from Rhizobium japonicum was purified. The subunit structure was found to be beta beta' alpha 2 alpha, with the following apparent molecular weights determined by electrophoresis: Mr (beta and beta') 150,000 each, Mr (sigma) 96,000, Mr (alpha) 40,000, Mr (holoenzyme) 490,000, Mr (core enzyme) 380,000. The recovery of sigma was 28%. RNA polymerase from aerobically grown R. japonicum cells and from nitrogen-fixing cells have the same electrophoretic properties suggesting that no chemical modification of the enzyme occurs when cells undergo this metabolic differentiation. The enzyme is Mg2+-dependent, rifampicin-sensitive, and has optimal activity at alkaline pH (8--10) and at 35--40 degrees C. It binds strongly to bacteriophage T7 promoters, weakly to antibiotic resistance genes, and not at all to cloned R. japonicum nif DNA. Preliminary in vitro transcription experiments, including nif DNA as template, revealed that additional factors may be required for selective transcription from promoters.

Electron microscopic studies of transcriptional complexes released from vaccinia cores during RNA-synthesis in vitro: methods for fractionation of transcriptional complexes

Electron microscopic (EM) and biochemical methods were employed to study the transcriptional complexes present in detergent lysates of vaccinia virus cores actively synthesizing RNA in vitro. When processed and examined in the EM, 14 'transcriptional sites' could be observed on full-length DNA templates. Fractionation of lysates by equilibrium density centrifugation in CsSO4, chromatography on hydroxyapatite columns or by sedimentation in sucrose gradients, allowed isolation of DNA templates associated with transcripts but these manipulations often resulted in fragmentation of the DNA template or promoted the release of transcripts from the template. It is suggested that RNA transcripts remain associated with the template in regions of supercoiling. These regions, in turn, may be maintained by DNA-protein interactions which are compromised as the transcriptional complexes are fractionated and purified.

Transcription in bacteriophage f1-infected Escherichia coli. Messenger populations in the infected cell

Transcription of bacteriophage f1 DNA in vivo occurs in two independent regions. They are separated from one another by a strong terminator just downstream from gene VIII on one side, and by the filamentous phage intergenic space on the other. One of these regions contains genes II, V, VII, IX and VIII, and is actively transcribed. In this region there are a number of promoters but only one effective terminator. Thus, most of the RNAs that come from this region overlap and share sequences close to the termination site. The other region, which contains genes III, VI, I and IV, is transcribed much less actively. This region gives rise to a long (approximately 4 X 10(3) bases) RNA that covers the entire region, and several RNAs that overlap in the region closest to their 5' termini. Several other RNAs appear to overlap only with the 4 X 10(3) base transcript. Thus, not only the frequency but the organization of transcription differs in the two portions of the genome.

Characterisation of the promoter for the LexA regulated sulA gene of Escherichia coli

The sulA gene of Escherichia coli, which encodes an inducible inhibitor of cell division, plays a role in the SOS response. Its expression, like that of other SOS genes, is repressed by the LexA protein. This paper reports the identification and characterisation of the promoter for the cloned sulA gene. The promoter bears good resemblance to the consensus promoter sequence and directs the synthesis of two major RNA species both in vitro and in vivo. Comparison of the sequence around the sulA promoter with the operator sequences of other SOS genes revealed the presence of an SOS box, the LexA protein binding site. This overlaps the -10 region of the promoter and covers the transcriptional initiation sites. LexA protein bound to this SOS box, would, therefore, effectively block transcription.

Preferential transfection with M13mp2 RF DNA synthesized in vitro

Single-strand DNA binding protein (SSB) from Escherichia coli abolishes transfection of E.coli by viral M13mp2 DNA at levels that inhibit transfection by M13mp2 replicative form (RF) DNA by approx. 25%. Synthesis of M13mp2 RF DNA (SS leads to DS) has been carried out using DNA polymerase I (Klenow fragment) and a unique 15-nucleotide primer. A time course for in vitro synthesis showed that the increase in transfection in the presence of SSB paralleled DNA synthesis after an initial lag period for transfection. Digestion of replication products with restriction endonucleases and S1 endonuclease indicates that only those molecules that are fully or almost fully duplex transfect competent cells in the presence of SSB.

Characterisation of the promoters for the ompA gene which encodes a major outer membrane protein of Escherichia coli

The regulatory region of the ompA gene from Escherichia coli has been characterized by biochemical and genetic approaches. Two overlapping promoters, P1 and P2, organized in that order with respect to the ompA coding sequence, were identified and it was found that ompA possesses an unusually long leader region. Both P1 and P2 were active in an in vitro transcription system although S1 mapping analysis of the ompA mRNA made in vivo showed that P2 was mainly responsible for transcription of the gene. Confirmation of this was obtained by studying down-promoter mutants of ompA cloned in pSC101. These mutants were classified into two groups, deletions and insertions. The deletions, which were caused by the IS102 insertion element found in pSC101 removed the--35 regions of both P1 and P2. However, since P2 was distally situated with respect to the IS element it was less extensively damaged and it is proposed that the residual P2 sequence is responsible for the low level of expression observed. In addition to an IS102 insertion in the promoter region four IS1 insertion mutants were characterized. These had integrated at different positions in the ompA leader region and were all incompletely polar.

The role of the components sigma and y of the DNA-dependent RNA polymerase of Lactobacillus curvatus in promotor selection

An average of 0.44 molecule each of the initiation factor sigma and the RNA polymerase binding protein y and 0.54 molecule of the subunit gamma per molecule of Lactobacillus curvatus DNA-dependent RNA polymerase have been found in the cell. Free factor y displaces sigma from free holo enzyme, E sigma. The formation of a binary complex from Ey, free sigma, and poly[d(A-T)], leads to immediate release of factor y. The release of the sigma factor occurs upon the transition of the binary to a ternary complex. A mixture of E and sigma forms binary complexes with all T7 DNA HpaII restriction fragments. In contrast a mixture of Ey and sigma binds selectively to promoter-containing DNA fragments, indicating that the stimulatory effect of y on transcription is due to an increase in the rate of promoter selection. The same RNA products are synthesised by E sigma and by Ey plus sigma with T7 DNA as template. Thus the nonspecific complexes formed by E sigma and T7 DNA are nonproductive. On the basis of these findings we propose a model for the transcription cycle in Lactobacillus curvatus.

Nucleotide sequence coding for the flavoprotein subunit of the fumarate reductase of Escherichia coli

The nucleotide sequence of the frdA gene, which encodes the flavoprotein subunit of the fumarate reductase, of Escherichia coli, has been determined. A polypeptide of Mr = 66,052, containing 602 amino acid residues, is predicted. In composition the FrdA protein strongly resembles the flavoprotein subunits of two succinate dehydrogenases. Moreover, a sequence of nine consecutive residues is common to the flavoprotein subunits from fumarate reductase and the beef heart succinate dehydrogenase. This sequence contains a histidyl residue which probably services as the site for attachment of the FAD cofactor to the reductase.

Nucleotide sequence and genome organisation of filamentous bacteriophages fl and fd

The DNA sequence of the filamentous phage F1, consisting of 6407 nucleotides, has been determined. When compared with the DNA sequence of the related filamentous phage fd (Beck et al., 1978), the f1 sequence is one nucleotide shorter and differs in 180 positions from the fd DNA. Only ten of these base exchanges cause amino acid exchanges in the known gene products. Most of the exchanges in f1 are the same as in M13 (Van Wezenbeek et al., 1980), showing a near identity of these two phage (there are only 59 nucleotide differences). Regulatory units for replication, transcription, and translation are in their essential parts identical in all three phage.

Efficient and selective initiation by yeast RNA polymerase B in a dinucleotide-primed reaction

Yeast RNA polymerase B catalyzes an efficient abortive initiation on double-stranded DNA templates using the appropriate combination of primer and substrate. The specificity of initiation was investigated using a recombinant plasmid (pJD14 DNA) containing the structural gene for yeast alcohol dehydrogenase I (ADHI). The combination of the dinucleotide UpA and UTP was 10 fold more efficient with pJD14 DNA than with the vector pBR322 DNA to direct the synthesis of the trinucleotide UpApU. Under these conditions, stable enzyme-DNA complexes were formed and could be retained on nitrocellulose filters. Using the UpA-primed system and a short pulse of RNA synthesis, transcription complexes were located on the yeast part of pJD14 DNA as evidenced by agarose gel electrophoresis. Southern hybridization of the pulsed RNA was restricted to a region, within the yeast DNA fragment, upstream to the initial region of the ADHI gene.

On the influence of thymidine analogues on the activity of phage fd promoters in vitro

RF I DNA of phage fd containing 5-bromo-deoxyuridine (br5Ud) or deoxyuridine (Ud) instead of deoxythymidine (Td) inthe codogenic strand was synthesized in vitro. The modified genomes could be cleaved by restriction endonuclease Hpa II. Although the recognition site of Hpa II is CCGG, the cleavage rate was significantly reduced with Ud-containing DNA. Both base substitutions altered the mobilities of several DNA fragments under the conditions of polyacrylamide gel electrophoresis. The fragments containing binding sites for RNA polymerase were assayed for the rates of stable complex formation. The substitution of Td for both, Ud and br5Ud, strongly influenced this parameter. Thus the methyl group of Td has to be regarded as one of the sites in DNA which determine the rate of stable RNA polymerase binding and thereby possibly mediate promoter activity in vitro (24,25,26). In most cases the rate of complex formation was decreased by Ud, but increased by br5Ud.

RNA-polymerase binding at the promoters of the rRNA genes of Escherichia coli

The promoter region of two bacterial rRNA genes was investigated by electron-microscopic analysis of polymerase binding, transcription initiation and nitrocellulose filtration of RNA-polymerase-DNA complexes, using restriction endonuclease generated fragments of recombinant plasmids and a transducing phage. The following observations have been made: 1. Two transcription initiation sites have been located approximately 200 and 300 base pairs upstream from the beginning of the sequence coding for mature 16 S rRNA. 2. Polymerase binding at these sites can be observed electronmicroscopically and a 360 base-pair fragment containing these sites binds to nitrocellulose in the presence of RNA-polymerase. This complex dissociates even at moderately high (0.1-0.2 M) salt concentrations. Although transcription initiation is reported to be more frequent at the first of these sites, the binding is much stronger at the second site. 3. In the case of the rrnD gene, BamHI cleaves a few base pairs upstream from the first transcription start site. This cleavage destroys polymerase binding at this site but does not influence binding at the second site. 4. At higher polymerase/DNA ratio four weak but distinct and regularly spaced binding sites can be observed preceding the two initiation sites at approximately 1000, 820, 640 and 440 base pairs before the mature 16 S rRNA sequence. 5. An extremely strong binding site is located about 1300 base pairs upstream from the beginning of the 16 S rRNA sequence. Very little (if any) initiation occurs at this site. The possibility is discussed that the noninitiating binding sites preceding the two transcription start points might functionally belong to the promoter region.

Nucleotide sequence of the filamentous bacteriophage M13 DNA genome: comparison with phage fd

The 6407 nucleotide-long sequence of bacteriophage M13 DNA has been determined using both the chemical degradation and chain-termination methods of DNA sequencing. This sequence has been compared with that of the closely related bacteriophage fd (Beck et al., 1978). M13 DNA appears to be only a single nucleotide shorter than fd DNA. There is an average of 3.0% of nucleotide-sequence differences between the two genomes, but the distribution of these changes is not random; the sequence of some genes is more conserved than of others. In contrast, the nucleotide sequences and positions of the regulatory elements involved in transcription, translation and replication appear to be identical in both filamentous phage DNA genomes.

Nucleotide sequence of the gene ompA coding the outer membrane protein II of Escherichia coli K-12

A nucleotide sequence of 2271 basepairs has been determined from cloned E. coli DNA which contains ompA. Withing that sequence, starting at nucleotide 1037, an open translational reading frame encodes a protein of 367 amino acids which starting with amino acid 22 agrees with the primary structure of protein II. The preceeding 21 amino acids constitute a typical signal sequence. There is a non-translated region of 360 nucleotides in front of the translational start. The insertion point of an IS1 element 110 nucleotides upstream from the start codon and an amber codon at the position of amino acid residue 28 have been localized in the DNA from two ompA mutants.

A versatile primer for DNA sequencing in the M13mp2 cloning system

A primer for DNA sequencing by the chain-termination method in the M13mp2 cloning system was constructed and amplified. The primer was isolated as an EcoRI/AluI restriction fragment. After conversion of the AluI end into an EcoRI end the fragment was cloned in pBR325 from which it can be recovered by cleavage with EcoRI. The primer hybridizes to the single-stranded DNA of the mature M13mp2 phage next to the site of insertion thereby directing DNA synthesis along the inserted DNA.

Construction and characterization of E. coli promoter-probe plasmid vectors. II. RNA polymerase binding studies on antibiotic-resistance promoters

The binding of Escherichia coli RNA polymerase to antibiotic-resistance promoters was examined using the nitrocellulose filter assay. Four filter-retainable HaeIII fragments were observed with pBR322 and the promoter-probe plasmids, pBRH1, pBRH2 and pBRH4. Of the three fragments studied, two were shown to carry promoters for the ampicillin (Ap) and tetracycline (Tc) resistance genes, while the third present in pBRH1 appears to be the promoter for colicin E1 immunity (Colimm). Although the formation of filter-retainable complexes involving the Tcr promoter was sensitive to high salt, Apr promoter complexes were not. It was also shown that plasmids containing only the "firm-binding" portion of the Tcr promoter could still bind RNA polymerase in vitro despite the fact that these plasmids confer no in vivo Tcr. Additional filter-binding experiments performed with AluI-digested pBR322 DNA revealed the presence of a fifth RNA polymerase binding site on pBR322. This site is probably the promoter for the 100 bp transcript thought to be involved in the initiation of plasmid replication. An analysis of the recombinant plasmid (pKTR25) which carries the Kan-B portion of the EcoRI kanamycin (Kn) resistance fragment revealed that this fragment contains two RNA polymerase binding sites. We believe that these sites are responsible for the insertional activation of the Tcr gene and may be the promoters for the Knr and fusidic acid (Fa) resistance genes.

Stable RNA-DNA-RNA polymerase complexes can accompany formation of a single phosphodiester bond

Incubation of RNA polymerase with poly[d(A-T)n] template results in a binary enzyme-DNA complex. Further addition of the dinucleotide UpA and [alpha-32P]UTP results in catalytic formation of the labeled trinucleotide UpApU until substrate exhaustion. In contrast, incubation of binary enzyme-DNA complexes with ApU and [alpha-32P]ATP results in labeled ApUpA formation to an extent that is stoichiometric with the amount of enzyme present despite an excess of substrates. The occurrence of ApUpA in a stable DNA-enzyme-RNA ternary complex is shown by gel exclusion chromatography, Millipore filtration, and the ability of ternary complexes to support subsequent RNA chain elongation. Radioactivity is not bound to Millipore filters when purified, labeled ApUpA is added to enzyme-DNA binary complexes. Hence, phosphodiester bond formation is required for stable ternary complex formation. The absence of the delta subunit of RNA polymerase or the addition of rifampicin to the reaction before ribonucleotide substrates results in catalytic ApUpA formation instead of stable ternary complexes.

Transcription of polyoma DNA by Escherichia coli RNA polymerase: influence of ionic strength on promoter selection

The influence of ionic strength on transcription of polyoma DNA by Escherichia coli RNA polymerase was investigated. At 0.15 M KCl, transcription was highly symmetrical and, due to the lack of reinitiation, a limited extent of RNA synthesis was observed. When the concentration of KCl was raised to 0.45 M, the affinity of the enzyme for its template, as well as its apparent affinity for ribonucleoside triphosphates, was reduced. Under optimal conditions, the rate and extent of RNA synthesis at 0.45 M KCl were greater than at 0.15 M KCl, and transcription was mostly asymmetric. Binding and initiation sites at both ionic strengths were identified; at 0.15 M KCl, transcription was initiated from two major sites, located at 0.99 and 0.06 map unit, whereas at 0.45 M KCl, a unique initiation site, at 0.99 map unit, was selected by RNA polymerase.

IS2-43 and IS2-44: new alleles of the insertion sequence IS2 which have promoter activity

The sequence of two new IS2 alleles with promoter activity (IS2-43 and IS2-44) is reported. The alleles are identical and are formed by a 17 bp tandem duplication in an AT-rich region of IS2. This created a new RNA polymerase binding site. A mutation was found that increased the frequency of formation of these 17 bp duplications but not of another class of duplications, the "mini-insertions". This suggested that the mechanisms of formation of the two classes of duplications are different.

Protein . nucleic-acid reaction kinetics. Theoretical analysis of the binding reaction between DNA and RNA polymerase

This paper presents methods developed in order to analyze experimental results concerning the binding of Escherichia coli DNA-dependent RNA polymerase to DNA at high and at low DNA concentrations, using the filter retention assay. The basis hypotheses, under which the mathematical expressions for describing the kinetics of binding are derived, are as follows. (a) At low DNA concentration: equivalence and independence of the specific binding sites; first-order dependence of the binding reaction on both DNA and protein concentration. (b) At high DNA concentration: equivalence and independence of the non-specific binding sites; no direct transfer or one-dimensional sliding of the protein along the DNA. Comparison between theoretical predictions and experimental results at high DNA concentration will allow one to determine the relative value of the rates of binding of RNA polymerase to different promoters (between 1 and 2 in T5 DNA). Binding experiments performed at low DNA concentration are reported in this paper: these results and the analysis which is reported allow one to determine the value of the rate constant of formation of non-filterable complexes for the system fd DNA (replicative form) . RNA-polymerase (kappa a = 3.3 X 10(8) M-1 s-1 in 0.1 M NaCl, 0.01 M MgCl2).

Escherichia coli RNA polymerase binding and initiation of transcription on fragments of lambda rifd 18 DNA containing promoters for lambda genes and for rrnB, tufB, rplC,A, rplJ,L, and rpoB,C genes

Promoters of genes for bacteriophage lambda and for Escherichia coli ribosomal RNA (rrnB), elongation factor Tu (tufB), ribosomal proteins L11 (rplK), L1 (rplA), L10 (rplJ), and L7/L12 (rplL), and RNA polymerase subunits beta (rpoB) and beta' (rpoC) were studied by use of two types of filter binding assays which measured E. coli RNA polymerase binding and initiation of transcription on restriction fragments of lambda rifd 18 DNA. The DNA fragments selectively retained on filters were eluted, concentrated, and analyzed by gel electrophoresis. The binding characteristics of these promotor fragments were qualitatively determined by varying the RNA polymerase, salt, and glycerol concentrations in the polymerase binding assay with HaeIII fragments of lambda rifd 18 DNA. The approximate map locations of these small HaeIII fragments were determined by HaeIII digestion of the larger, previously mapped EcoRI, HindIII, and SmaI restriction fragments of the phage DNA. The base compositions proximal to the 5' ends of mRNA's from promoters on these DNA fragments were elucidated by the polymerase initiation assay, in which the addition of various combinations of nucleoside triphosphates to the reaction allowed RNA polymerase to form high-salt-resistant initiation complexes with some of the known SmaI + EcoRI, EcoRI + HindIII, or HaeIII restriction fragments of lambda rifd 18 DNA. The data obtained by this technique are consistent with the map positions and 5' mRNA base sequences of the known lambda promotors p'R, po, pR and pL. In the main focus of this work, we have determined the approximate map locations and 5' mRNA base compositions of several promoters for known E. coli genes including rrnB, tufB, rplK,A, and rplJ,L. No promoter was detected between rplL and the rpoB,C genes. Thus our data are consistent with the conclusion of Yamamoto and Nomura (1978) that the beta and beta' mRNA is probably cotranscribed from the promoter for rplJ,L. Finally, the approximate map positions and the NTP combinations which initiated transcription of several unknown lambda and E. coli in vitro promoters are reported. The methods reported should prove useful for studying the characteristics of promoters on other cloned DNA regions.

The structure of a transcriptional unit on colicin E1 plasmid

In an RNA-synthesizing system in vitro, a low-molecular-weight RNA consisting of about 110 residues (RNA-I) was efficiently synthesized on DNA of colicin E 1 plasmid (ColE1) and its deletion derivatives. The promoter site for RNA-I was analysed by testing the RNA polymerase-binding ability and template activity of restriction fragments; it was mapped in the region between the replication initiation site and the colicin immunity gene of ColE1. The direction of transcription was determined by hybridization tests to the separated strands of the template. The DNA region directing RNA-I was sequenced, and RNA-I was assigned on the sequence based on the nearest-neighbour data of RNA. The sequences of its promoter and terminator regions were also deduced. Although the function of this small RNA species is unknown, a unique secondary structure could be constructed from its sequence and sensitivity to RNase.