Mechanism of ethidium bromide inhibition of RNA polymerase

Nanoformulation of a Trypanocidal Drug Isometamidium Chloride Ameliorates the Apurinic-Apyrimidinic DNA Sites/Genotoxic Effects in Horse Blood Cells

Isometamidium chloride (ISM) is a trypanocide for the prophylactic and therapeutic use against vector-borne animal trypanosomosis (mainly Surra caused by Trypanosoma evansi) and African animal trypanosomosis caused by T. congolense/T. vivax/T. brucei). ISM was found to be an efficient trypanocide for therapeutic/prophylactic use against trypanosomosis; however, it produces some local and systemic detrimental effects in animals. We synthesized isometamidium chloride-loaded alginate gum acacia nanoformulation (ISM SANPS) to lessen the detrimental side effects of isometamidium chloride (ISM) while treating trypanosomal diseases. We intended to determine the cytocompatibility/toxicity, and DNA deterioration/chromosomal structural or number changes (genotoxicity) of ISM SANPs using mammalian cells in a concentration-dependent manner. Apurinic/apyrimidinic (AP) sites are one of the major types of DNA lesions formed during base excision and repair of oxidized, deaminated, or alkylated bases. The intensity of the cellular AP site is an excellent marker of the deterioration of DNA quality. We thought it pertinent to quantify the AP sites in ISM SANPs-treated cells. Our investigations established a dose-dependent cyto-compatibility or toxicity and DNA impairment (genotoxicity) in ISM SANPs-treated horse peripheral blood mononuclear cells. ISM SANPs were biocompatible at various concentrations tested on the mammalian cells.

Mitochondrial homeostatic disruptions are sensitive indicators of stress in neurons with defective mitochondrial DNA transactions

Neurodegeneration and mitochondrial dysfunction are closely linked across many clinical conditions. In genetic diseases that result from defects in mitochondrial DNA (mtDNA) synthesis or maintenance, neurodegeneration is a frequent and major component of the disease pathology. In sporadic neurodegenerative diseases such as Alzheimer's and Parkinson's disease, mtDNA defects have been observed clinically. Mitochondrial stress related to mtDNA dysregulation can produce neuronal dysfunction and death via impaired electron transport chain activity, which results in deficient ATP production and related increases in mitochondrial reactive oxygen species (ROS) production. However, mtDNA dysregulation in post-mitotic neurons may also produce disturbances in mitochondrial homeostasis that are known to impair neuronal function as well. In this study, we used sub-toxic doses of ethidium bromide (EtBr) to induce mtDNA-associated mitochondrial stress in primary cortical neurons and measured several aspects of mitochondrial homeostasis, mitochondrial function and cell death. We found that low-dose EtBr severely depletes mtDNA synthesis and mitochondrial mRNA levels. Furthermore, homeostatic processes are especially disrupted in toxin treated neurons while mitochondrial function is relatively preserved. Mitochondria become fragmented and motility is abolished, while respiration and mitochondrial polarization are partially maintained. Moreover at these doses, cells do not exhibit increased ROS production, clear neurite retraction or loss of viability. These results indicate that mitochondrial homeostasis is a sensitive marker of mtDNA associated stress compared to mitochondria-functional outputs or endpoints related to cellular toxicity. These homeostatic disruptions are expected to contribute to neuronal dysfunction and potentially drive neurodegenerative disease pathology.

Impact of DNA damaging agents on genome-wide transcriptional profiles in two marine Synechococcus species

Marine microorganisms, particularly those residing in coastal areas, may come in contact with any number of chemicals of environmental or xenobiotic origin. The sensitivity and response of marine cyanobacteria to such chemicals is, at present, poorly understood. We have looked at the transcriptional response of well characterized Synechococcus open ocean (WH8102) and coastal (CC9311) isolates to two DNA damaging agents, mitomycin C and ethidium bromide, using whole-genome expression microarrays. The coastal strain showed differential regulation of a larger proportion of its genome following “shock” treatment with each agent. Many of the orthologous genes in these strains, including those encoding sensor kinases, showed different transcriptional responses, with the CC9311 genes more likely to show significant changes in both treatments. While the overall response of each strain was considerably different, there were distinct transcriptional responses common to both strains observed for each DNA damaging agent, linked to the mode of action of each chemical. In both CC9311 and WH8102 there was evidence of SOS response induction under mitomycin C treatment, with genes recA, lexA and umuC significantly upregulated in this experiment but not under ethidium bromide treatment. Conversely, ethidium bromide treatment tended to result in upregulation of the DNA-directed RNA polymerase genes, not observed following mitomycin C treatment. Interestingly, a large number of genes residing on putative genomic island regions of each genome also showed significant upregulation under one or both chemical treatments.

Caenorhabditis elegans, a pluricellular model organism to screen new genes involved in mitochondrial genome maintenance

The inheritance of functional mitochondria depends on faithful replication and transmission of mitochondrial DNA (mtDNA). A large and heterogeneous group of human disorders is associated with mitochondrial genome quantitative and qualitative anomalies. Several nuclear genes have been shown to account for these severe OXPHOS disorders. However, in several cases, the disease-causing mutations still remain unknown. Caenorhabditis elegans has been largely used for studying various biological functions because this multicellular organism has short life cycle and is easy to grow in the laboratory. Mitochondrial functions are relatively well conserved between human and C.elegans, and heteroplasmy exists in this organism as in human. C. elegans therefore represents a useful tool for studying mtDNA maintenance. Suppression by RNA interference of genes involved in mtDNA replication such as polg-1, encoding the mitochondrial DNA polymerase, results in reduced mtDNA copy number but in a normal phenotype of the F1 worms. By combining RNAi of genes involved in mtDNA maintenance and EtBr exposure, we were able to reveal a strong and specific phenotype (developmental larval arrest) associated to a severe decrease of mtDNA copy number. Moreover, we tested and validated the screen efficiency for human orthologous genes encoding mitochondrial nucleoid proteins. This allowed us to identify several genes that seem to be closely related to mtDNA maintenance in C. elegans. This work reports a first step in the further development of a large-scale screening in C. elegans that should allow to identify new genes of mtDNA maintenance whose human orthologs will obviously constitute new candidate genes for patients with quantitative or qualitative mtDNA anomalies.

Complex-formation of Ethidium Bromide with poly[d(A-T)].poly[d(A-T)]

The interaction of Ethidium Bromide (EtBr) with double-stranded (ds-) and single-stranded (ss-) poly[d(A-T)] was studied in different ionic strengths solutions. Optical spectroscopy and Scatchard analysis results indicate that the ligand interacts to both helix and coiled structures of the polynucleotide by "strong" and "weak" binding modes. The association parameters (binding constant -K- and the number of nucleotides corresponding to a binding site -n) of the strong type of interaction were found to be independent of Na+ concentration. Weak interaction occurs at low ionic strength and/or high EtBr concentration. Estimated binding parameters of EtBr with ss- and ds-polynucleotide are in good agreement with those for EtBr-B-DNA complexes. Data obtained provided an evidence for a stacking interaction of EtBr with single stranded poly[d(A-T)].

The in vitro effects of isometamidium chloride (Samorin) on the piscine hemoflagellate Cryptobia salmositica (Kinetoplastida, Bodonina)

Isometamidium chloride (Samorin) is therapeutic in rainbow trout (Oncorhynchus mykiss) during preclinical and chronic cryptobiosis. However, the toxic mechanism of isometamidium on Cryptobia salmositica has not been elucidated. The objective of the present study was to examine the in vitro effects of isometamidium on C. salmositica. Under in vitro conditions, isometamidium chloride reduced the infectivity of C. salmositica suspended in whole fish blood. It accumulated rapidly in the kinetoplast (within 1 min) and caused disruption and decantenation of kinetoplast DNA. The in vitro cryptobiacidal activity of isometamidium was reduced when parasites were incubated in medium containing serum supplement, suggesting that isometamidium also binds to plasma proteins. Isometamidium altered glycoprotein receptors (epitopes) for antibodies on the surface of C. salmositica and thus protected some of the parasites from lysis by complement-fixing antibodies. In vitro oxygen consumption and carbon dioxide production decreased in drug-exposed C. salmositica, with increased products of glycolysis, i.e., lactate and pyruvate, after exposure to isometamidium. This suggests that some C. salmositica switched from aerobic respiration to glycolysis when the mitochondrion was damaged by isometamidium.

Pharmacology of existing drugs for animal trypanosomiasis

Lack of much interest by the pharmaceutical industry to venture into development of new antitrypanosomal drugs has been a major stimulus to an intensification of research into the few existing drugs. Those indicated for animal trypanosomiasis include: isometamidium, homidium and diminazene, used primarily against Trypanosoma congolense, T. vivax and T. brucei; and quinapyramine, mainly indicated for use against T. evansi infections. A great deal of research effort has focused on development of pharmacological and parasitological methodologies, which have considerably advanced our understanding on the efficacy, resistance, disposition and toxicological mechanisms of these drugs. While a clinical breakthrough has been made in the recent past, in the field of chemotherapy of T. evansi infections by the introduction of a new arsenic compound, melarsenoxide cysteamine, chemotherapy of T. simiae infections in pigs still remains a major challenge because the existing drugs are either ineffective or too toxic for economic use. Further research into the existing drugs is a prerequisite for their optimal usage in the overall effort of improving animal health and productivity through control of trypanosomiasis.

Inhibition of DNA-dependent RNA synthesis by 8-methoxypsoralen

The effect of the photobinding of 8-methoxypsoralen to phage T7 DNA on different steps of RNA synthesis in vitro was assayed. Total RNA synthesis is reduced to a few percent and the transcript size is decreased, as shown by means of gel filtration on a Sepharose 4B column when DNA of the adduct content of six drug molecules per 10(3) nucleotides is used. The initiation of RNA chains seems to be less affected, as inferred from an abortive initiation assay. Synthesis of pppApU on DNA of the same adduct content is inhibited to 34% of the corresponding controls, while the overall RNA synthesis is inhibited to 6%. The amount of the enzyme needed for maximal retention of DNA, the kinetics of its binding and the decay of the polymerase-DNA complex at high ionic strength (or on decrease of the temperature) are similar with DNA either irradiated in the absence of the drug or DNA bearing six 8-methoxypsoralen molecules per 10(3) nucleotides. It is concluded from this study that 8-methoxypsoralen partially inhibits initiation and blocks movement of RNA polymerase along the template, inducing premature termination. It does not appear to influence the binding of the enzyme to DNA.

Intercalating drugs and low temperatures inhibit synthesis and processing of ribosomal RNA in isolated human mitochondria

Mitochondrial DNA transcription in isolated HeLa cell mitochondria faithfully reproduces the in vivo process. In this system, actinomycin D, proflavine and ethidium bromide preferentially inhibit the formation of ribosomal RNA over that of messenger RNA, strongly supporting independent controls of the two overlapping transcription units involved in their synthesis. The processing step removing the tRNAPhe sequence at the 5' end of the ribosomal RNA precursor is uniquely sensitive to low temperature, proflavine and ethidium bromide.

In vitro effects of acridine intercalation on RNA polymerase interactions with supercoiled DNA

In vitro transcription of supercoiled DNA by purified E. coli RNA polymerase was inhibited by Acridine Orange in a bimodal manner while N-10 benzyl substituted Acridine Orange is about one-third as inhibitory and effects monophasic inhibition. The inhibition correlates with the supercoil unwinding abilities of these two intercalators with Acridine Orange unwinding supercoiled DNA at 1/3 the concentration required for the substituted acridine orange. Direct visualization of DNA-RNA polymerase complex on agarose gels showed that these intercalators directly interfere with this association and the more effective the drug is in unwinding DNA supercoils the more effective it is in interfering with the DNA-enzyme complex. In addition, specific intercalators differentially affect the stability of DNA-RNA polymerase-RNA ternary complexes.

Purification and properties of an endonuclease from the mitochondrion of Saccharomyces cerevisiae

An endonuclease, which is found only in the mitochondrion of the yeast Saccharomyces cerevisiae, has been purified. The protein has a sedimentation coefficient of 6.3 S, equivalent to a molecular weight of 105,000. The enzyme is active at pH 7.6, when it degrades single-stranded DNA about 10-times faster than double-stranded DNA, but at pH 5.4 only double-stranded DNA is degraded. In both cases the enzyme acts endonucleolytically, breaking a single phosphodiester bond at a random location within the DNA substrate. Mn2+ or Mg2+ are required for activity; Ca2+ and Zn2+ are ineffective cofactors. Enzyme activity at pH 7.6 is severely inhibited by low concentrations of NaCl or KCl, while activity at pH 5.4 is unaffected by salt. Ethidium bromide inhibits both the DNase activity at pH 5.4 and the activity with single-stranded DNA at pH 7.6, but has no effect on the DNase activity with double-stranded DNA at pH 7.6.

Type I DNA topoisomerases from mammalian cell nuclei interlock strains and promote renaturation of denatured closed circular PM2 DNA

Type I DNA topoisomerases from mouse ascites cell nuclei and from rat liver cell nuclei act on denatured viral closed circular PM2 DNA to produce molecules with a highly contracted structure as well as fully duplex non-supercoiled covalently closed circular molecules. Highly contracted DNA molecules contain a novel type of topological linkage in which a strand in one region of the double-stranded molecule passes between the strands in another region of the circular molecule one or more times. Since it is also found that the action of the topoisomerase promotes renaturation of complementary strands in denatured closed circular DNA, it is suggested that formation of contracted DNA structures proceeds through renatured, duplex intermediates with highly negative superhelix densities that contain small single-stranded regions.

Ethidium bromide-mediated renaturation of denatured closed circular DNAs. The nature of denaturation-resistant fractions of bacteriophage PM2 closed circular DNA

Addition of the intercalating dye ethidium bromide (EtdBr) to a solution of alkali-denatured double-stranded closed circular PM2, PhiX174, or lambdab(2)b(5)c phage DNAs, under conditions such that the solution remains strongly alkaline, can result in the renaturation of up to 100% of the DNA upon neutralization of the solution. For a fixed time of incubation of the alkaline dye-containing solution before neutralization, there exists a minimum concentration of the dye below which no EtdBr-mediated renaturation is observed for each species of closed circular DNA examined. These minimum concentrations increase, for a given DNA, with increasing ionic strength and temperature. The kinetics of accumulation of forms renaturing upon neutralization of alkaline solutions, at fixed concentrations of dye and DNA, are dependent upon the molecular weight and superhelix density of the starting DNA. After extended periods of incubation at a fixed ionic strength and temperature, however, the profiles of percentage of DNA renatured as a function of ethidium concentration become very similar for all the closed circular DNAs tested and display a transition from an absence of dye-mediated renaturation to virtually 100% renaturation upon neutralization over a small range of dye concentration. Circular DNA containing one or more strand scissions remains strand-separated under all the conditions used to effect the renaturation of closed circular DNA. These findings indicate that configurations of closed circular DNA, in which at least some of the complementary bases are apposed, can be selectively stabilized and accumulate in the presence of ethidium in solutions containing 0.19 N hydroxide ion. The closed circular DNA of bacteriophage PM2 has properties distinct from those of the other DNAs of this study in that it has been shown to contain fractions which exist in the base-paired duplex form after neutralization of strongly alkaline solutions of this DNA incubated at ambient temperature, while no duplex DNA is observed after exposure to alkali and neutralization of solutions of closed circular DNA from other sources. (1,2) The fraction of denaturation-resistant PM2 DNA is shown in the present work to depend upon the temperature and time of incubation in alkali, but not upon the superhelix density of the starting DNA. PM2 closed circular DNA also behaves anomalously with respect to its kinetics of accumulation of forms renaturing upon neutralization of alkaline, EtdBr-containing solutions. Evidence is presented that the translocation of one of the strands of a closed circular molecule relative to the other, which is required for the molecule to exist in the denatured form at neutral pH, is a process to which PM2 DNA is less labile than the other closed circular DNAs of this study.

A rapid method for the purification of supercoiled PM2 DNA by affinity chromatography on H1 histone covalently coupled to agarose

A simple and rapid method is described for the purification of supercoiled PM2 DNA by affinity chromatography on columns of H1 histone covalently coupled to agarose. The method does not require the use of intercalating agents or ultracentrifugation procedures. Under the conditions most appropriate for purification, elution is carried out in a single step with buffered 0.7 M NaCl after the sample has been loaded onto the column in buffered 0.2 M NaCl. The DNA eluted at the higher salt concentration consists of supercoiled closed circular DNA at greater than 90% purity independently of the ratio of supercoiled to nicked circular DNA in the input mixture.

Studies on the biosynthesis of bacterio-opsin. Demonstration of the existence of protein species structurally related to bacterio-opsin

1. The kinetics of processing newly synthesized bacterio-opsin from the non-crystalline state within the brown membrane to the crystalline state within the purple membrane was followed by pulse-chase experiments. 2. Biosynthesis of bacterio-opsin was found to be highly resistant to RNA-synthesis inhibitors like rifampicin and ethidium bromide. In the presence of ethidium bromide, only five protein species continue to be synthesized in halobacteria, one of them being bacterio-opsin. 3. In spheroplasts, synthesis of bacterio-opsin is found to be selectively disturbed. The purple membrane isolated from spheroplasts contains new, additional protein species with apparent molecular weights of 19 000, 23 000 and 29 000. These proteins share common amino acid sequences with bacterio-opsin. 4. In the halobacterial cell membrane, two membrane proteins with apparent molecular weights of 30 000 and 36 000 were detected which are structurally related to bacterio-opsin. 5. Bacterio-opsin as well as the 30 000 Mr and 36 000-Mr proteins contain covalently bound sulphate.

Action of intercalating agents on the activity of DNA polymerase I

The effect of intercalating compounds such as 9-aminoacridine, quinacrine (atebrin), proflavine and daunomycin on the activity of DNA polymerase I(EC 2.7.7.7) was studied in vitro and compared with the binding of these acridines to native DNA. The enzyme kinetics were followed at various concentrations of DNA 3'-OH primer end groups and constant concentrations of deoxynucleosidetriphosphates as well as under the opposite conditions. The Km values for the DNA 3'-OH end groups were 16--38 nM and for the deoxynucleosidetriphosphates 2--5 micrometer, depending on the buffer and pH used in the enzymatic assay. All acridine derivates inhibit the DNA polymerase; at variable DNA concentrations a competitive inhibition was observed, where the Ki values ranged between 0.87 and 8.5 micrometer. At variable concentrations of deoxynucleosidetriphosphates and constant DNA concentration a non-competitive inhibition was observed. On denatured 3'-OH DNA as well as on poly(dA) - (dT)10 as substrate no inhibition by 9-aminoacridine was observed. 5'--3' exonuclease activity of DNA polymerase is inhibited by 9-aminoacridine but 3'--5' exonuclease activity on denatured DNA is not influenced by this intercalating compound. The affinity of the acridines to DNA was determined spectrophotometrically under conditions similar to those in the enzymatic assay and the computed frequency of intercalation was related to the inhibition of enzymatic activity. The mechanism of inhibition is explained by a disturbance of the structure of the double helical DNA due to the interaction of the bound acridine derivates.

Bacteria with defective rho factors suppress the effects of N mutations in bacteriophage lambda

A prediction based on the model for N-gene function of bacteriophage lambda proposed by Roberts (1971) is confirmed by showing that a lambdaN- double mutant is able to grow in strains of E. coli with defective rho transcription termination factors. The burst sizes for lambdaN- in these strains range from 5 to 24% the burst sizes for lambdaN+ in the same strain. This low level of suppression is also evident in the levels of synthesis of the lambda exonuclease and is consistent with other evidence that the defect in the rho factors of these strains is only partial. These strains do not suppress the effects of mutations in genes O, P and Q of lambda nor in genes 30 and 43 of bacteriophage T4. The lack of suppression of lambdaQ- is significant because the Q-gene product, like the N-gene product, is believed to function as an anti-terminator of lambda transcription but at termination sites that may not require rho factor action.

X-ray diffraction studies of circular superhelical DNA at 300-10,000-A resolution

X-ray diffraction studies on circular superhelical DNA from bacteriophage PM2 at a very low scattering angle show that it is possible to measure the superhelical scattering function of the molecule. The results suggest that in addition to the primary supercoil, a higher order of supercoiling of the DNA is present, an effect which can be interpreted with a simple analogue.

Daunorubicin inhibition of DNA-dependent RNA polymerases from Ehrlich ascites tumor cells

Two different forms of DNA-dependent RNA polymerase have been solubilized and purified from nuclei of Ehrlich ascites tumor cells. The purification procedure involves ammonium sulfate precipitation and gel filtration on Sephadex G-25. The separation of A and B activities is achieved by chromatography on DEAE-cellulose. Nuclei are prepared from cells, sensitive or resistant to daunorubicin. RNA polymerases A and B have an absolute requirement of divalent cations for activity. Native DNAs are better templates than heat-denatured DNAs for RNA polymerase A. On the contrary heat-denatured DNA is more transcribed than the native one by RNA polymerase B. The low level of transcription of total and nucleolar ascites DNAs is due to the DNA, the same results being obtained with ascites and calf thymus RNA polymerases A and B. The inhibitory action of daunorubicin on RNA polymerases A and B from Ehrlich ascites tumor cells has been studied in vitro. The same results are obtained with enzymes extracted from sensitive or resistant cells. Daunorubicin does not inhibit the binding of RNA polymerases to the DNA template, but prevents the transformation of the DNA-daunorubicin-RNA-polymerase unstable complex into the highly stable one. This inactive ternary complex has a dissociation rate faster than the stable complex formed without daunorubicin. The size of the RNA synthesized in the presence or absence of daunorubicin is the same.

In vitro system for induction of delayed early RNA of bacteriophage T4

Concentrated lysates of Escherichia coli that had been infected with bacteriophage T4 in the presence of chloramphenicol show the same restriction of transcription in vitro as is found in vivo. Restricted lysates can be complemented with lysates from infected cells to induce production of delayed early RNA. Complementation takes place between the RNA polymerase of the restricted lysate and the DNA of the unrestricted lysate. We present evidence that delayed early RNA in these lysates is initiated at quasi-late (middle) promoters, and that such recognition is related to changes in the state of the template DNA.

Circular dichroism studies of ethidium bromide binding to the isolated nucleolus

Circular dichroism in the 300-360 nm region and fluorescence induced by intercaltating binding of ethidum bromide to both DNA and RNA components were studied in isolated HeLa nucleoli. Both DNA and RNA compoents contribute to the induced dichroic elliticity. Digestion of nucleoli by RNase or DNase shows that most of the induced ellipticity comes from the DNA component. In nucleoli with an RNA/DNA = 0.8/1.0 the RNA component gives only 20% of the total ellipticity when measured at an ethidium bromide/DNA = 0.25. Spectro-fluorometric titration shows that ethidium bromide intercalates mostly into DNA in nucleoli. Both circular dichroism and fluorescence studies indicate that both DNA and RNA components in isolated nucleoli are less accessible to intercalating binding by ethidium bromide when compared to purified nucleolar DNA, DNA in chromatin or purified ribosomal RNA. Circular dichroic measurements of intercalating binding of ethidium bromide to to nucleoli may be used to study changes in nucleoli under different physiological or pathological conditions.

Distribution of intercalative dye binding sites in chromatin

Actinomycin D (AMD) and ethidium bromide (EB) were found to bind to chromatin isolated from a variety of gander tissues according to a strong and weak process analogous to that found for deproteinized DNA. Distribution of the dye intercalation sites in chromatin and DNA were evaluated at low r-values (dye bound per nucleotide) by following the appearance of free dye released from chromatin and DNA during thermal denaturation. The AMD dissociation profiles closely resembled the DNA or chromatin-DNA denaturation profiles; whereas the EB derivative dissociation profiles, indicated 3 major transitions for transcriptionally active chromatin with the main component corresponding to the single component which characterizes DNA. The DNA-like component was greatly reduced for mature erythrocyte chromatin but could be generated by removal of histone I and V. Removal of residual non acid-soluble proteins from dehistonized chromatin, urea treatment or dissociation and reconstitution of chromatin favoured conversion to the DNA-like component with loss of the other two. This study indicates that more than one type of binding exists generally in chromatin.

Diacridines: bifunctional intercalators. III. Definition of the general site of action

Electron microscopy of HeLa cells exposed to spermine diacridine shows nucleolar distortions which disappear after several days despite the persistence of the metabolic changes promoted by spermine diacridine. This compound inhibits ribosomal RNA synthesis and appears to act independently of any particular phase of the cell cycle. The DNA content of the HeLa cells remains unchanged and the cell distribution is not significantly disturbed from its normal distribution in the various phases of the cell cycle. Spermine diacridine and other diacridines inhibit primarily chain initiation but also chain elongation by DNA-directed RNA polymerase of Azotobacter vinelandii.

Transcription termination factor rho activity is altered in Escherichia coli with suA gene mutations

Rho factor has been purified from a strain of E. coli containing the Su78 mutation in the suA gene and assayed in another strain with an amber mutation in the suA gene. The rho from the Su78 mutant strain is present in normal amounts but has altered termination function; it does not terminate transcription at some sites that are recognized effectively by the rho factor from the isogenic wild-type strain. Rho in cells with an amber mutation in the suA gene has been assayed by its RNA-dependent ATPase activity. Extracts of cells of this strain have only 9% as much of this rho activity as extracts of cells of the isogenic wild-type strain. These results suggest that rho is the product of the suA gene. Since mutations in the suA gene are known to decrease polar effects of mutations in other genes, it is also suggested that rho factor is at least partially responsible for polar effects.

Isolation and purification of RNA polymerases from rye embryos

A procedure has been developed for the purification of soluble DNA-dependent RNA polymerase (EC 2.7.7.6) from rye embryos. The enzyme solubilized by high salt extraction with sonication and resolved by DEAE-cellulose chromatography yields two activities. Enzyme I eluted at 0.15 M (NN4)2SO4, was insensitive to alpha-amanitin and was extremely labile. Enzyme II eluted at 0.25 M (NH4)2SO4 was inhibited by alpha-amanitin. However, DEAE-Sephadex chromatography yields three DNA-dependent RNA polymerases. Enzyme I is resistant to amanitin, while II and III enzymes are inhibited by this poison. Partially purified on DEAE-cellulose, polymerase II was further purified by hydrophobic chromatography on an omega-aminobutyl-Sepharose column. After omega-aminobutyl-Sepharose chromatography, enzyme II was stable and was more active with denatured than with native DNA as template. The activity of purified RNA polymerase II is dependent on the DNA, Mn-2+ and Mg-2+ added and requires ATP, GTP, CTP and UTP for its maximum activity. Transcription is inhibited besides by alpha-amanitin, by chromomycin A3, daunomycin, ethidium bromide and actinomycin D. Rifampin and rifamycin SV do not inhibit the enzyme. Synthetic copolymers were also effective as templates.

DNA-dependent RNA polymerase from Pseudomonas BAL-31. I. Purification and properties of the enzyme

The DNA-dependent RNA polymerase from Pseudomonas BAL-31, the host for bacteriophage PM2, has been purified 154-fold using differential centrifugation, chromatography on DEAE-cellulose, ammonium sulfate precipitation, and sucrose gradient centrifugations at low and high ionic strength. The resulting enzyme is free of enzyme activities which could interfere with transcription studies and is greater than 85% pure as judged by polyacrylamide gel electrophoresis. Like other bacterial RNA polymerases, its subunit structure is beta'beta sigma alpha2. From gel electrophoresis the beta', beta, and alpha subunits have approximately the same molecular weights as those from Escherichia coli, whereas the sigma subunit is 5% larger (89,000 vs. 85,000). A summation of the subunits yields a molecular weight of 485,000 for the holoenzyme. Like other bacterial RNA polymerases, it sediments as a monomer (15 S) at low ionic strength (0.065) and as a dimer (22 S) at high ionic strength (0.75). Its activity is stimulated three-fold by monovalent cations (K+,NH4+, NA+) with additional stimulation provided by divalent cations (Mg2plus, Mn2plus). The transcription of phage PM2 form I (supercoiled) DNA has an ionic strength optimum of 0.26 for continuous long-term synthesis, and over an ionic strength range of 0.09-0.46 "plateau-type" kinetics are not observed. The sigma subunit is required for optimal PM2 transcription. The enzyme is sensitive to the same inhibitors of transcription as the RNA polymerase from E. coli, it has a temperature optimum of 28 degrees, and it is 50% inactivated by heating 10 min at 41 degrees. It has template preference similar to E. coli polymerase and shows little preference for homologous templates. With various DNAs the order of template activities is T7 greater than PM2 I congruent to T4 greater than PM2 II (relaxed circular form) greater than lambda-c greater than calf thymus greater than BAL-31 DNA. Phage PM2 form I DNA is transcribed at a twofold greater rate than PM2 form II DNA by this enzyme.