A COMPLEX OF ENZYMATICALLY SYNTHESIZED RNA AND TEMPLATE DNA

Transcription termination

Chromosomes are organized into units of expression that are bounded by sites where transcription of DNA sequences into RNA is initiated and terminated. To allow for efficient stepwise assembly of complete transcripts, the transcribing enzyme (RNA polymerase) makes a stable complex with the DNA template until it reaches the terminator. Three general mechanisms of transcription termination have been recognized: one is by a spontaneous dissociation of the RNA at a sequence segment where RNA polymerase does not maintain its usual stable interaction with the nascent chain; another involves the action of a protein (rho factor in bacteria) on the nascent RNA to mediate its dissociation; and a third involves an action triggered by a protein that binds to the DNA at a sequence that is just downstream of the termination stop point. Transcription termination is important in the regulation of gene expression both by modulating the relative levels of various genes within a single unit of expression and by controlling continuation of transcription in response to a metabolic or regulatory signal.

Conformational alterations of transcription termination protein rho induced by ATP and by RNA

Transcription termination protein rho from Escherichia coli possesses an RNA-dependent ATP hydrolysis activity necessary for expression of its termination function. We have used the rate of trypsin-mediated inactivation of ATPase activity as a conformational probe to test for ligand binding-induced conformational changes in the rho polypeptide. When present in molar excess over rho polypeptide, trypsin inactivates rho ATPase by a first order process that correlates well with the loss of intact rho polypeptide. When rho protein binds poly(C) or poly(dC), its susceptible bonds become more accessible to trypsin action. On the other hand, when rho binds either ATP or ADP those bonds become less accessible. These results suggest that rho protein assumes an altered conformation when an RNA cofactor is bound and that is assumes a distinctly different conformation when a nucleotide substrate or product is bound. A special change in the accessibility of trypsin-susceptible bonds is also detected when rho in its complex with poly(C) is catalyzing the hydrolysis of ATP.

Electron microscopic analysis of transcription: mapping of initiation sites and direction of transcription

An electron microscope technique is described that allows rapid characterization of transcription in vitro. DNA is transcribed with Escherichia coli RNA polymerase in vitro, and the RNA is hybridized to its template. Measurement of the resulting transcription R-loop molecules allows accurate mapping of transcription initiation sites (promoter sites) and analysis of the direction and rate of transcription and the level of transcription from each initiation site. The two major early promoters pR and pL of bacteriophage lambda have been mapped within 0.1-0.3 map units of the known positions and three additional sites have been confirmed. Six transcription initiation sites have been preliminarily mapped on plasmid pSF2124 DNA.

A possible mechanism responsible for the correction of transcription errors

Nucleoside triphosphate phosphohydrolase (NTPase) activity was found in a preparation of E. Coli RNA polymerase. This enzymatic activity is capable of hydrolysing all four ribonucleoside triphosphates to the nucleoside diphosphates. However, during in vitro RNA synthesis directed by poly(dC) or poly(dT), only the non-complementary nucleoside triphosphate of the same heterocyclic class was hydrolysed. No incorporation of the non-complementary precursor into RNA could be detected in these experiments. When another RNA polymerase preparation, devoid of NTPase activity, was employed, there was no hydrolysis of any nucleoside triphosphate and significant incorporation of non-complemtary precursor into RNA was observed. These observations lead us to the conclusion that NTPase, acting in conjunction with RNA polymerase, has the function of correcting errors in transcription.

Orotic acid excretion in some wild-type strains of Escherichia coli K-12

During rapid growth, the excretion of pyrimidines, predominantly uracil, is a common phenomenon in procaryotes and eucaryotes. In Escherichia coli, some K-12 strains excrete orotic acid and not uracil. This is caused by a mutation in the pyrF gene.

Photochemical crosslinking of transcription complexes with psoralen. I. Covalent attachment of in vitro SV40 nascent RNA to its double-stranded DNA template

14C-labeled SV40 DNA has been transcribed with E. coli RNA polymerase using 3H-labeled ribonucleotide triphosphates as precursors. The resulting transcription complexes were then photochemically crosslinked with the psoralen derivative, 4'-aminomethyl-4,5', 8-trimethylpsoralen (AMT), at 37 degrees C and analyzed in SDS-sucrose gradients. It was found that the photochemical crosslinking procedure caused the nascent RNA chains to co-sediment with their double-stranded (helical) SV40 templates in the denaturing sucrose gradient. This result and several control experiments suggest that covalent linkages have formed between nascent RNA and helical DNA after the photochemical reaction. The crosslinking phenomenon was observed to be independent of the superhelical state of the DNA used as the template. Prior addition of EDTA to stop the transcription is not required for successful crosslinkage.

Studies on the transcription complex of Escherichia coli RNA polymerase

To study the chain elongation phase of enzymatic RNA synthesis ternary transcription complexes with T7 DNA or poly[dA) - (dT)] as template were isolated by gel exclusion chromatography. The DNA in these complexes contains single-stranded regions which are recognized by a single-strand-specific nuclease from Neurospora crassa. The non-codogenic DNA strand in the poly[(dA) - (dT)] ternary complex is preferentially hydrolysed by the nuclease. The polymerase protects predominantly the codogenic strand in this complex from digestion by DNAse I. In the T7 DNA ternary complex a DNA fragment with a chain length of approximately 26 nucleotides and an RNA fragment of about 22 nucleotides are protected by polymerase from digestion by DNAse and RNAse.

In vitro transcription of three different ribosomal RNA cistrons of E. coli; heterogeneity of control regions

Ribosomal RNA synthesis from three different rRNA cistrons of E. coli, located on different phage DNAs was compared and found to have the same characteristics as regards chain length, salt and temperature dependence and the effect of ppGpp. However, some clear and reproducible quantitative differences between rRNA synthesis from the different templates both in presence and absence of ppGGpp were found. Rifampicin and heparin experiments showed that these differences were located at the initiation sites. We propose that heterogeneity exists in the RNA polymerase binding regions of the rRNA prmoters in E. coli.

Studies of DNA bound RNA molecules isolated from nucleoids of Escherichia coli

Methods are developed for studying RNA molecules bound directly to DNA in bacterial nucleoids. It is found that among the 1000-3000 nascent RNA chains that normally are attached to the DNA via their associated RNA polymerase molecules, 74 +/- 14 chains per nucleoid can be bound differently. These chains unlike the other nascent RNAs remained bound to the DNA after the chromosome was deproteinized and sheared. Sensitive assays using radioactive labels detected no RNA polymerase involved in the RNA-DNA linkage. The linkage was stable at low temperatures, but the RNA separated from the DNA at high temperature. The bound RNA molecules were heterodisperse (weight average length 1200 bases). Pulse-chase experiments and studies of the fate of these RNA molecules in rifampicin treated cells demonstrated that they are nascent RNAs, degraded or released from the DNA in vivo with kinetics similar to that of the total nascent RNA. Hybridization analyses showed that the chains are composed at least in part of nascent rRNA and known mRNA molecules. Some, but not more than 5% of the bound chains, contained sequences of about 300 nucleotides in length, bound to the DNA in an RNase resistant form.

Preparations and properties of ribonucleic acid polymerase from Acinetobacter calcoaceticus

Deoxyribonucleic acid (DNA)-dependent ribonucleic acid (RNA) polymerase (EC 2.7.7.6) from Acinetobacter calcoaceticus was purified to apparent homogeneity and its properties were compared with those of the Escherichia coli B enzyme. The molecular weights of the two native active enzymes as well as their alpha and beta subunits appeared to be similar. No subunit corresponding to that of sigma from E. coli was found, and furthermore no separation between the beta subunits could be detected by gel electrophoresis. A number of different DNAs were transcribed by the enzyme from A. calcoaceticus. Maximal RNA synthesis occurred at pH 8.7, 10 mM Mg2+, or 0.3 mM Mn2+ and at a total ionic strength of 0.1. Higher ionic strengths led to increasing inhibition of transcription and at mu = 0.4 complete inhibition was observed. The mechanism of inhibition of salt was not related to the initiation event as observed with T4 core RNA polymerase (R.Kleppe, 1975). In an attempt to understand the mechanism of inhibition by salt, the effect of ionic strength on the sedimentation properties of the enzyme was investigated. At low ionic strength, enzyme species with sedimentation coefficients, s20,w, of 5.8S, 12.4S, and 19.3S were present. In buffers with higher ionic strengths the relative amounts of the 12.4S species decreased. It is suggested, therefore, that the inhibition of activity at higher salt concentrations is caused by a decrease in concentration of the active enzyme species.

Isolation and properties of the transcription complex of Escherichia coli RNA polymerase

A procedure is described which permits complete separation of a transcription complex formed with template DNA, growing RNA chain and functioning RNA polymerase, from RNA polymerase molecules which have bound to DNA but not initiated RNA synthesis. The method is based on the marked stability of the transcription complex to dissociation by high concentrations of CsCl or CS2SO4 which enable banding the complex after equilibrium centrifugation. With use of the newly developed procedure, affinity of Escherichia coli RNA polymerase to T7 phage DNA was found to increase during initiation of RNA synthesis but then decrease concomitant with elongation of RNA chain presumably due to migration of the enzyme to DNA sites of weak affinity. Under the conditions of maximum affinity, the transcription complex contained one core polymerase for each T7 DNA if it was isolated by centrifugation in CsCl; in contrast, 2-6 enzyme molecules remained attached on the complex when the centrifugation was carried out in Cs2SO4. Thus, RNA polymerases bound to different sites of transcription initiation appear to be distinguished based on the affinity of interaction. Attempts are also described to isolate the transcription complex in vivo by Cs2SO4 centrifugation by Brij 58-deoxycholate lysate of lysozyme-treated Escherichia coli cells. The isolated complex contained approx. 50 polymerase molecules per Escherichia coli genome as well as other unidentified proteins.

Structure and function of the genome of coliphage T5. Transcription in vitro of the "nicked" and "nick-free" T5+ DNA

Purified T5+ DNA in nicked form and after repair of the specific single-strand interruptions with DNA ligase was used in transcription studies using Escherichia coli RNA polymerase (holoenzyme) in the presence and absence of E. coli termination protein rho. The transcriptional products were analyzed with respect to their size distribution and the sequences transcribed from the different templates. The results indicate that the single-strand breaks in the DNA of bacteriophage T5, though in genetically defined positions, do not have any specific effect on transcription in vitro. Furthermore, the E. coli rho protein, although it depresses net RNA synthesis and reduces the average molecular weight of the transcripts, seems to act in a non-specific way in this system.

Transcriptional regulation of T4 bacteriophage-specific enzymes synthesized in vitro

In contrast to dihydrofolate reductase and four other phage-specific enzymes, the initiation of deoxynucleotide kinase is essentially prevented if rifampin is added to a culture of Escherichia coli B cells within 1.5 min after infection with T4. Deoxynucleotide kinase thus belongs to a group of so-called delayed-early enzymes that is not initiated from an immediate-early promoter site. We prepared crude extracts from infected cells in a manner designed to maintain the integrity of the complexes of native, endogenous T4 DNA with bacterial structural and enzymatic units concerned with RNA synthesis. The initiation of the synthesis of the mRNA for dihydrofolate reductase, an example of an immediate-early enzyme, and deoxynucleotide kinase, a special type of delayed-early enzyme, was studied with these extracts prepared from cells infected in the absence or presence of chloramphenicol. Initiation of transcription of the dihydrofolate reductase gene is immediate when programmed by extracts made either from cells treated with chloramphenicol prior to infection (CM extracts) or from cells 3 min into the normal infection cycle (3-min extracts). However, initiation of transcription of the deoxynucleotide kinase gene programmed by CM extracts is delayed 2 min relative to the immediate initiation of transcription of the deoxynucleotide kinase gene programmed by 3-min extracts. These experiments duplicated in vitro effects of the antibiotics on the synthesis of phage-specific mRNA previously noted only in vivo.

Studies on deoxyribonucleic acid-dependent ribonucleic acid polymerase from Escherichia coli. Variations of the enzyme activity during growth

1. RNA polymerase activity of Escherichia coli extracts prepared from cells in exponential and stationary phases of growth, when measured in the presence and absence of external template, showed significant qualitative differences. 2. In both extracts, polymerase activity was higher when assayed with external template, suggesting the presence of a pool of enzyme not bound to cellular DNA. 3. In the crude extract, the fraction of enzyme bound to cellular DNA is higher during the exponential phase of growth. 4. A method is described for the purification of enzyme molecules not tightly bound to cellular DNA from exponential- and stationary-phase cultures. 5. Purified enzyme preparations showed differences in template requirement and subunit composition. 6. On phosphocellulose chromatography of stationary-phase enzyme, a major portion of polymerase activity eluted from the column with 0.25m-KCl. In the case of exponential-phase enzyme, polymerase activity eluted from a phosphocellulose column mainly with 0.35m-KCl. 7. Enzyme assays done with excess of bacteriophage T(4) DNA showed a strong inhibition of stationary-phase enzyme by this template. The exponential-phase enzyme was only slightly inhibited by excess of bacteriophage T(4) DNA.

Ribosomal RNA synthesis in vitro: a protein-DNA complex from Bacillus subtilis active in initiation of transcription

A protein-DNA transcription complex, isolated from logarithmic-phase cells of Bacillus subtilis, is active in the initiation of new rounds of RNA synthesis in vitro. Transcription directed by the endogenous DNA of the complex is sensitive to inhibitors of initiation. In addition, the effect of addition of a competing template indicates that RNA polymerase in the complex is bound to endogenous DNA in a dissociable, preinitiation state. Hybridization-competition analysis of the RNA product obtained from the in vitro reaction indicates that it is greatly enriched for ribosomal RNA sequences. This initiating complex should be useful for the study of regulation of expression of ribosomal RNA genes.

Reinitiation of RNA synthesis on transcription of chromatin DNA by Escherichia coli RNA polymerase

The transcription of DNA in chromatin by Escherichia coli RNA polymerase resembles that of isolated DNA in two important respects: the release of nascent RNA and reinitiation of RNA synthesis is dependent on the salt concentration, and RNA synthesis is markedly stimulated by the addition of ribosomes.