The structure and mechanism of action of bacterial DNA-dependent RNA polymerase

Overproduction and purification of highly active recombinant Pseudomonas aeruginosa str. PAO1 RNA polymerase holoenzyme complex

The bacterial RNA polymerase (RNAP) is a large, complex molecular machine that is the engine of gene expression. Despite global conservation in their structures and function, RNAPs from different bacteria can have unique features in promoter and transcription factor recognition. Therefore, availability of purified RNAP from different bacteria is key to understanding these species-specific aspects and will be valuable for antibiotic drug discovery. Pseudomonas aeruginosa is one of the leading causes of hospital and community acquired infections worldwide - making the organism an important public health pathogen. We developed a method for producing high quantities of highly pure and active recombinant P. aeruginosa str. PAO1 RNAP core and holoenzyme complexes that employed two-vector systems for expressing the core enzyme (α, β, β', and ω subunits) and for expressing the holoenzyme complex (core + σ⁷⁰). Unlike other RNAP expression approaches, we used a low temperature autoinduction system in E. coli with T7 promoters that produced high cell yields and stable protein expression. The purification strategy comprised of four chromatographic separation steps (metal chelate, heparin, and ion-exchange) with yields of up to 11 mg per 500 mL culture. Purified holoenzyme and reconstituted holoenzyme from core and σ⁷⁰ were highly active at transcribing both small and large-sized DNA templates, with a determined elongation rate of ~18 nt/s for the holoenzyme. The successful purification of the P. aeruginosa RNAP provides a gateway for studies focusing on in vitro transcriptional regulation in this pathogen.

DNA-melting at the Bacillus subtilis flagellin promoter nucleates near -10 and expands unidirectionally

A central step in promoter activation by RNA polymerase (RNAP) is the localized separation of the DNA strands to form the transcription bubble. We have used potassium permanganate footprinting to monitor DNA strand-separation by the Bacillus subtilis sigmaD RNAP at the strong promoter, Phag, directing transcription of flagellin. The susceptibility of individual thymine bases to permanganate oxidation is influenced by temperature, Mg2+, nucleotides, and the RNAP delta subunit. In the absence of delta, sigmaD RNAP establishes a partially opened complex even at 0 degrees C with permanganate reactivity localized between -11 and -4 (RP(-4)). The region of strand separation expands to near -1 at 20 degrees C (RP(-1)) and to +3 at 40 degrees C (RP(+3)). The delta subunit inhibits the downstream propagation of the transcription bubble and thereby increases the concentration of early intermediates in the melting pathway. Indeed, E delta sigmaD forms a distinct nucleated complex (RPn) at 0 degrees C with a structural distortion localized to an AT base step within the -10 element. We propose a model for promoter melting in which strand separation nucleates within the conserved -10 consensus and subsequently propagates downstream. Mg2+ and nucleoside triphosphates (NTPs) favor the downstream propagation of the transcription bubble and strongly stimulate the RP(-1) to RP(+3) conversion. The NTP effects are apparently mediated by binding of substrate to the initiating NTP site: purines are more effective than pyrimidines and GMP alone can greatly increase the level of DNA-melting. The binding of substrates, but not Mg2+ alone, can effectively overcome the anti-melting effect of delta.

Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA

Escherichia coli RNA polymerase is able to site-specifically melt 12 bp of promoter DNA at temperatures far below those normally associated with DNA melting. Here we consider several models to explain how RNA polymerase destabilizes duplex DNA. One popular model proposes that upon binding to the promoter, RNA polymerase untwists the spacer DNA between the -10 and -35 regions, which results in a destabilization of the -10 region at a TA base step where melting initiates. Promoter untwisting may result, in part, from extensive wrapping of the DNA around RNA polymerase. Formation of the strand-separated open complex appears to be facilitated by specific protein-DNA interactions which occur predominantly on the non-template strand. Recent evidence suggests that these include important contacts with sigma factor region 2.3, which we propose binds the displaced single strand of DNA.

The DNA replication fork can pass RNA polymerase without displacing the nascent transcript

Replication proteins encoded by bacteriophage T4 generate DNA replication forks that can pass a molecule of Escherichia coli RNA polymerase moving in the same direction as the fork in vitro. The RNA polymerase ternary transcription complex remains bound to the DNA and retains a transcription bubble after the fork passes. The by-passed ternary complex can resume faithful RNA synthesis, suggesting that the multisubunit RNA polymerase of E. coli has evolved to retain its transcript after DNA replication, allowing partially completed transcripts to be elongated into full-length RNA molecules.

Identification of a nucleic acid-binding region within the largest subunit of Drosophila melanogaster RNA polymerase II

The largest and the second-largest subunit of the multisubunit eukaryotic RNA polymerases are involved in interaction with the DNA template and the nascent RNA chain. Using Southwestern DNA-binding techniques and nitrocellulose filter binding assays of bacterially expressed fusion proteins, we have identified a region of the largest, 215-kDa, subunit of Drosophila RNA polymerase II that has the potential to bind nucleic acids nonspecifically. This nucleic acid-binding region is located between amino acid residues 309-384 and is highly conserved within the largest subunits of eukaryotic and bacterial RNA polymerases. A homology to a region of the DNA-binding cleft of Escherichia coli DNA polymerase I involved in binding of the newly synthesized DNA duplex provides indirect evidence that the nucleic acid-binding region of the largest subunit participates in interaction with double-stranded nucleic acids during transcription. The nonspecific DNA-binding behavior of the region is similar to that observed for the native enzyme in nitrocellulose filter binding assays and that of the separated largest subunit in Southwestern assays. A high content of basic amino acid residues is consistent with the electrostatic nature of nonspecific DNA binding by RNA polymerases.

The RNA polymerase II ternary complex cleaves the nascent transcript in a 3'----5' direction in the presence of elongation factor SII

The process by which RNA polymerase II elongates RNA chains remains poorly understood. Elongation factor SII is known to be required to maximize readthrough at intrinsic termination sites in vitro. We found that SII has the additional and unanticipated property of facilitating transcript cleavage by the ternary complex. We first noticed that the addition of SII caused a shortening of transcripts generated by RNA polymerase II at intrinsic termination sites during transcription reactions in which a single NTP was limiting. Truncation of the nascent transcript was subsequently observed using a series of ternary complexes artificially paused after the synthesis of 15-, 18-, 20-, 21-, and 35-nucleotide transcripts. Transcripts as short as 9 or 10 nucleotides were generated in 5-min reactions. All of these shortened RNAs remained in active ternary complexes because they could be chased quantitatively. Continuation of the truncation reaction produced RNAs as short as 4 nucleotides; however, once cleavage had proceeded to within 8 or 9 bases of the 5' end, the resulting transcription complexes could not elongate the RNAs with NTP addition. Transcript cleavage requires a divalent cation, appears to proceed primarily in 2-nucleotide increments, and is inhibited by alpha-amanitin. The catalytic site of RNA polymerase II is repositioned after transcript cleavage such that polymerization resumes at the proper location on the template strand. The extent and kinetics of the transcript truncation reaction are affected by both the position at which RNA polymerase is halted and the sequence of the transcript.

Parameters affecting transcription termination by Escherichia coli RNA. II. Construction and analysis of hybrid terminators

Rho-independent terminators are characterized by two major functional regions, one upstream from the termination site having a sequence capable of forming an RNA hairpin in the nascent transcript, the second extending, from the base of this hairpin, seven to nine nucleotides along the transcript to the actual sites of termination (3'-tail region). This latter region of the transcript is often rich in uridine residues. Both regions are postulated to play central roles in the termination process. We have constructed a series of hybrid rho-independent, transcription terminators in which sequences upstream and downstream from the RNA hairpin for the Escherichia coli trp attenuator (trpatt+) are interchanged with sequences from trpatt mutant (1419) or from the phage T7 early terminator (T7Te). Similar hybrids have been constructed for T7Te, replacing flanking sequences with trpatt regions. The effects of such changes on transcription termination have been tested in vitro with purified E. coli RNA polymerase to determine the intrinsic termination efficiency (%T) of each hybrid terminator. Both the trpatt+ terminator and T7Te are highly efficient rho-independent terminators in vitro. However, replacement of trpatt+ sequences upstream and downstream from the RNA-terminator hairpin with the comparable T7Te sequences reduces %T dramatically, suggesting that the RNA-terminator hairpin does not function independently from its flanking regions. Regions downstream from the actual termination/release site are shown to be of considerable importance in determining %T for terminators bearing the T7Te or trpatt1419 3'-tail region, but have little effect on terminators with the trpatt+ 3'-tail region. For terminators bearing the T7Te or trpatt1419 3'-tail region that are inefficient, efficient termination is restored by elevated concentrations of KCl in the reaction. The results do not fit well with models for termination in which %T is determined by a two-step process in which the terminator-RNA hairpin, and a seven to 12 base-pair DNA-RNA hybrid structure rich in uridine residues, act independently to cause the polymerase to pause, and to release the transcript, respectively. DNA sequences both upstream and downstream from these regions, as well as DNA sequences downstream from the transcript termination site, can significantly affect the termination process. Conversely, terminators lacking a 3'-tail region rich in uridine residues can be highly efficient, but only when joined with appropriate sequence immediately downstream from the termination site. This suggests that the 3'-tail region acts in some manner other than the formation of an unstable DNA-RNA hybrid that facilitates termination.

Parameters affecting transcription termination by Escherichia coli RNA polymerase

Escherichia coli RNA polymerase can terminate transcription efficiently at rho-independent terminators in a purified transcription system in the absence of accessory factors. This process of "intrinsic termination" involves direct recognition of the terminator by the core RNA polymerase, and provides an important model system for the study of the molecular interactions involved in the switch between elongation and termination. We have analyzed the intrinsic termination efficiency (%T) of 13 rho-independent terminators, under a variety of in vitro reaction conditions. Although all of these sites share the general sequence features of typical rho-independent terminators, we find a wide range of %T (2% to 90%) for the different sites under our standard transcription conditions. While %T for a particular site is characteristic of that site, the efficiency can be altered considerably by the nature and concentration of salts in the reaction, by alteration of the concentrations of the nucleoside triphosphate substrates, or by transcription from supercoiled rather than linear templates. Surprisingly, different conditions can alter %T to a different extent for different terminators. For neutral salts such as potassium chloride or potassium glutamate, changes in the range from 0.1 to 1 M affect %T for different terminators in a distinct manner, depending on the terminator and the anion involved. At some sites, %T is greatly increased by Cl- concentrations up to 1 M, while at other sites %T is reduced or unaffected by these conditions. At some sites K+ concentrations up to 1 M give a modest increase in %T, while at other sites %T is slightly reduced under the same conditions. Thus the actual values of %T, as well as the order of terminator sites ranked according to %T, can be altered greatly according to the choice of reaction conditions. Reduction of the Mg2+ concentration below 1 mM has a dramatic and quite different effect, enhancing termination to approximately 100% for all terminators tested. Transcription of supercoiled DNA templates gives somewhat reduced %T as compared with linear DNA templates. However, the effect is no greater than twofold. Our results are not consistent with those expected for models in which %T is determined by the differential stability of DNA, RNA and hybrid duplex structures at the melted region in the transcription complex. Thus, the Cl anion does not affect the stability of nucleic acid duplexes even at 1 M concentrations, but can enhance termination tenfold. Also, the alterations of monovalent cation concentration that affect %T are not expected to have a differential effect on Tm for DNA, RNA and hybrid duplexes.(ABSTRACT TRUNCATED AT 400 WORDS)

Immunoelectron microscopy of enzymes, multienzyme complexes, and selected other oligomeric proteins

The collective term "immunoelectron microscopy" subsumes a number of techniques in which the biological material is decorated with specific antibodies, prior to being visualized in the electron microscope. In this article, we have reviewed literature on immunoelectron microscopy that focusses on the analysis of the molecular architecture of proteins, in particular of enzymes and of multienzyme complexes. Molecular immunoelectron microscopy has been remarkably successful with multi-subunit enzymes of complex quaternary structures, and in many cases the data have been the basis for the eventual development of detailed three-dimensional molecular models. The elucidation of subunit composition and juxtaposition of a given enzyme, an important accomplishment in itself, has in turn stimulated and guided discussions on the catalytic mechanism; illustrative examples include F1 ATPase and citrate lyase, among others. Here we have chosen a variety of enzymes, multienzyme complexes, and non-enzymatic proteins to demonstrate the versatility of immunoelectron microscopy, to illustrate methodological prerequisites and limitations, and to discuss significance and implications of individual immunoelectron microscopy studies.

Spontaneous cleavage of RNA in ternary complexes of Escherichia coli RNA polymerase and its significance for the mechanism of transcription

Ternary complexes of RNA polymerase, bearing the nascent RNA transcript, are intermediates in the synthesis of all RNAs and are regulatory targets of factors that control RNA chain elongation and termination. To study the catalytic and regulatory properties of RNA polymerases during elongation, we have developed methods for the preparation of these intermediates halted at defined positions along a DNA template. To our surprise, some of these halted complexes undergo a reaction in which the RNA transcript is cleaved up to 10 nucleotides from its 3'-terminal growing point. The 5'-terminal fragment, bearing a free 3'-OH residue, remains bound to the RNA polymerase-DNA complex and can resume elongation, whereas the 3'-terminal oligonucleotide of 2-10 nucleotides, bearing a 5'-phosphate, is released. RNA cleavage occurs only in the ternary complex and requires a divalent metal ion such as Mg2+. Since RNA polymerases are believed to have a single catalytic site for nucleotide addition, this reaction is unlikely to be due to hydrolysis catalyzed by this site comparable to the 3'----5' exonuclease activity associated with the catalytic center found for some DNA polymerases. Nor is this reaction easily explained by models for transcription elongation that postulate a 12-base-pair DNA.RNA hybrid as intermediate. Instead, we suggest that this is an unusual kind of protein-facilitated reaction in which tight binding of the RNA product to the enzyme strains the RNA phosphodiester linkage, resulting in cleavage of the RNA well away from the catalytic center. By this model, the nascent RNA enters a product binding site beginning 3 or 4 nucleotides from the growing point at the 3' terminus. This RNA binding site extends for up to 16 nucleotides along the protein surface. The stress brought about by this binding appears to vary considerably for different ternary complexes and may play a role in driving the translocation of the RNA polymerase along the DNA.

Footprinting analysis of mammalian RNA polymerase II along its transcript: an alternative view of transcription elongation

Ternary complexes of RNA polymerase II, bearing the nascent RNA transcript, are intermediates in the synthesis of all eukaryotic mRNAs and are implicated as regulatory targets of factors that control RNA chain elongation and termination. Information as to the structure of such complexes is essential in understanding the catalytic and regulatory properties of the RNA polymerase. We have prepared complexes of purified RNA polymerase II halted at defined positions along a DNA template and used RNase footprinting to map interactions of the polymerase with the nascent RNA. Unexpectedly, the transcript is sensitive to cleavage by RNases A and T1 at positions as close as 3 nucleotides from the 3'-terminal growing point. Ternary complexes in which the transcript has been cleaved to give a short fragment can retain that fragment and remain active and able to continue elongation. Since DNA.RNA hybrid structures are completely resistant to cleavage under our reaction conditions, the results suggest that any DNA.RNA hybrid intermediate can extend for no more than 3 base pairs, in dramatic contrast to recent models for transcription elongation. At lower RNase concentrations, the transcript is protected from cleavage out to about 24 nucleotides from the 3' terminus. We interpret this partial protection as due to the presence of an RNA binding site on the polymerase that binds the nascent transcript during elongation, a model proposed earlier by several workers in preference to the hybrid model. The properties of this RNA binding site are likely to play a central role in the process of transcription elongation and termination and in their regulation.

Plasma clearance, organ distribution and target cells of interleukin-6/hepatocyte-stimulating factor in the rat

The plasma half-life of recombinant human interleukin-6 (rhIL-6) was determined in rats by measuring the disappearance of the biological activity as well as of the radioactivity of 125I-rhIL-6 from the circulation. The kinetics of clearance were biphasic. It consisted of a rapid initial disappearance corresponding to a half-life of 3 min, and of a second slow one corresponding to a half-life of about 55 min. By cellulose-acetate electrophoresis it was shown that rhIL-6 binds to a plasma protein resulting in a complex migrating in the beta-gamma region; 20 min after intravenous injection, about 80% of the 125I-rhIL-6 that had disappeared from the circulation was found in the liver. 125I-rhIL-6 was exclusively localized on the surface of parenchymal cells suggesting the existence of an interleukin-6 receptor on the hepatocytes.

Nucleotide sequence analysis of a gene cloned from Leptospira biflexa serovar patoc which complements an argE defect in Escherichia coli

The genus Leptospira, as a member of the order Spirochaetales, forms one of the most ancient evolutionary branches of the eubacteria. These spirochetes are morphologically and physiologically different from most eubacteria, and little is known about Leptospira genetics. In this communication, we report the first nucleotide sequence of a Leptospira gene. A gene which complements an argE mutation in Escherichia coli was isolated from a plasmid-based genomic library composed of Leptospira biflexa serovar patoc DNA. The functional region for the complementing activity was localized by transposon mutagenesis and restriction enzyme mapping and by subcloning. Nucleotide sequence analysis indicated a single open reading frame within the region containing argE complementing activity. The size of the predicted protein, 31,071 daltons, was in excellent agreement with data obtained from coupled transcription-translation reactions primed with cloned L. biflexa DNA. One surprising result was that the predicted amino acid sequence of this protein closely resembles portions of the beta' subunits of RNA polymerases from bacteria and chloroplasts.

Transcription initiation by Escherichia coli RNA polymerase at the gene II promoter of M13 phage: stability of ternary complex, direct photocrosslinking to nascent RNA, and retention of sigma subunit

The initial stages of transcription have been characterized using a template containing the gene II promoter region of M13 phage. Initiation of transcription in the presence of all four nucleotides gives rise to the 140-residue run-off transcript, with a minor pause at the RNA hexamer stage. Cycling, leading to the accumulation of significant amounts of short oligonucleotides [1], was not observed. An RNA hexamer GUUUUU was the sole product when GpU and UTP were used and the ternary complex with the hexamer was stable and resistant to high salt (0.4 M) and S1 nuclease attack. After direct ultraviolet photocrosslinking of the RNA hexamer to RNA polymerase in the ternary complex, the radioactive label incorporation into various subunits was determined by autoradiography after sodium tetradecyl sulfate gel electrophoresis to be as follows: sigma, 86%; beta, 14%; beta' and alpha, negligible. Both electrophoresis and sucrose gradient centrifugation experiments indicate that the sigma subunit is not released from the ternary complex when either the RNA hexamer or the 140-residue RNA is synthesized on this template, even though the complexes are stable.

Kinetics of the stages of transcription initiation at the Escherichia coli lac UV5 promoter

The kinetics of initiation by Escherichia coli RNA polymerase on the lac L8UV5 promoter was studied by a gel retardation method that separates protein-DNA complexes from free DNA. The binding constant of the closed complex, the forward and reverse rate constants of isomerization from closed to open complex, and the forward rate constant from the open to initiated complex were measured. Both the forward and reverse isomerization rates were found to be temperature dependent, and the activation energies for these steps were determined. The rates of open complex formation and dissociation were not affected by the addition of ribonucleotide triphosphates; however, the extent of dissociation was greatly reduced if the triphosphates added allowed a short, unstable RNA product to form. The dissociation rate was not affected by heparin, a polyanion competitor that sequesters the polymerase. The rate of initiated complex formation appeared to be dependent on whether the initiating moiety was a mononucleotide triphosphate or dinucleoside monophosphate and on the sequence of the dinucleoside. These results are compared to those found on both the lac L8UV5 and other bacterial and phage promoters by less direct measurements. We use the values obtained for the individual rate constants to investigate the predicted steady-state kinetics of initiation-limited transcription, with the conclusion that the rate-limiting step is formation of the open complex in the limit of low polymerase concentration. However, when RNA polymerase is saturating, the rate is determined by the transition from open complex into the stably initiated ternary complex.(ABSTRACT TRUNCATED AT 250 WORDS)

Abortive and productive elongation catalysed by purified spinach chloroplast RNA polymerase

Experimental conditions are reported under which purified spinach chloroplast RNA polymerase catalyses the abortive elongation reaction on a synthetic poly[d(A-T)] template. The reaction only occurs under very stringent conditions and absolutely requires Mn2+ as the metal activator. No reaction can be detected in the presence of Mg2+. Furthermore, the rate of abortive elongation with the chloroplast enzyme is extremely sensitive to the presence of added salts, such as KCl or (NH4)2SO4, in the reaction assays. In the combined presence of Mn2+ and Mg2+, a marked inhibition of abortive elongation is associated with an activation of productive elongation and an increased length of RNA chains. Thus, whereas Mn2+ is more active than Mg2+ for phosphodiester bond formation, it appears that Mg2+ favors the stabilization of the ternary transcription complexes. These results are compared with those obtained under similar conditions for wheat germ RNA polymerase II and Escherichia coli RNA polymerase.

Effect of low nucleotide concentrations on abortive elongation catalysed by wheat-germ RNA polymerase II

A kinetic study of the effect of elongating nucleotide concentration on the reactions of abortive elongation catalysed by wheat-germ RNA polymerase II on a poly[d(A-T)] template suggests that the shift from abortive to productive elongation may involve the participation of at least two nucleotides, according to a mechanism very similar to that reported for Escherichia coli RNA polymerase. Experiments performed with non-complementary nucleotides with respect to the DNA template, and with substrate derivatives, allow an analysis of the substrate specificity during these reactions. Similar experiments performed with poly[d(A-A-T)].poly[d(T-T-A)] as template provide a starting point for a better understanding of the effect of DNA sequence on the rates of abortive and productive elongation catalysed by the plant enzyme.

Probable insensitivity of mollicutes to rifampin and characterization of spiroplasmal DNA-dependent RNA polymerase

The effect of rifampin on five mollicutes (Spiroplasma citri, Spiroplasma melliferum, Spiroplasma apis, Acholeplasma laidlawii, and Mycoplasma mycoides) was compared with that on Escherichia coli. We found that, in contrast to wild-type E. coli, mollicutes were insensitive to rifampin. DNA-dependent RNA polymerases from S. melliferum and S. apis were purified to the stage where the enzymes were dependent on the addition of exogenous templates for activity. The enzymes were then tested for their sensitivity to rifampin. Spiroplasmal enzymes were at least 1,000 times less sensitive to rifampin than the corresponding E. coli enzyme. This result provides a molecular basis for the resistance of mollicutes to rifampin. The RNA polymerase of S. melliferum was further purified and its subunit composition was investigated. The RNA polymerase has one small and two large subunits. The structure of S. melliferum RNA polymerase therefore resembles that of the eubacterial enzymes in spite of its insensitivity to rifampin.

Synthesis and properties of adenosine-5'-triphosphoro-gamma-1-(5-sulfonic acid)naphthyl ethylamidate: a fluorescent nucleotide substrate for DNA-dependent RNA polymerase from Escherichia coli

A new fluorescent ATP analog, adenosine-5'-triphosphoro-gamma-1-(5-sulfonic acid)naphthyl ethylamidate (gamma-1,5-EDANS)ATP, containing the fluorophore N-(aminoethyl)-5-naphthylamine-1-sulfonic acid attached via a gamma-phosphoamidate bond was synthesized in good yield. It has absorption maxima at 255 and 344 nm and a fluorescence emission maximum at 490 nm. These spectral characteristics permit its uses as an energy acceptor for energy transfer from the intrinsic protein fluorophores and as an energy donor for the energy transfer to the intrinsic Co of Co-substituted RNA polymerases. This analog is a good substrate for Escherichia coli RNA polymerase and can be used to initiate the RNA chain. Incorporation of this analog into the total RNA synthesized was about 60% of that observed for ATP, independent of the templates used. Its Km values (22 and 118 microM) are twofold higher and its Vmax values (45 and 59 nmol/min/mg of enzyme) are 40% lower than those for ATP using calf thymus DNA and poly[d(A-T)], respectively, as template. For abortive initiation reaction using pAR1435 plasmid DNA as template, the Km and Vmax values of this analog are 2.7 times higher and 7 times lower, respectively, than those of ATP. With its desirable spectroscopic properties, (gamma-1,5-EDANS)ATP is a good probe for the studies of nucleotide-protein interactions, active site mapping of RNA polymerase, and other ATP-utilizing biological systems.

Poly(dAT) dependent trinucleotide synthesis catalysed by wheat germ RNA polymerase II. Effects of nucleotide substrates and cordycepin triphosphate

Kinetics of condensation of ribonucleotides to dinucleotides, leading to trinucleotide products formation, have been studied using wheat germ RNA polymerase II and poly(dAT). Assay conditions can be selected under which both ApUpA and UpApU are formed in catalytic amounts. The kinetic parameters associated with these reactions indicate that the rate of trinucleotide formation might be affected by DNA sequence, as reported for E.coli RNA polymerase. Kinetics of disappearance of ApUpA and UpApU were studied under experimental conditions allowing poly(rAU) synthesis. The results can be interpreted as if after formation of a phosphodiester bond, a slow isomerisation step of the ternary transcription complex could occur. During this step, transcription complexes could dissociate with a finite probability, releasing trinucleotides in an abortive pathway. The above results are discussed in the view that, under these experimental conditions, wheat germ RNA polymerase II catalyses poly(rAU) synthesis, as if it is a non-processive enzyme. Cordycepin triphosphate can be condensed to a dinucleotide primer, yielding ApUpA. However the ATP analogue cannot be incorporated into longer products than a trinucleotide. On the other hand 3'-dATP behaves as a very potent inhibitor of translocation, with an inhibition constant of 0.15 microM, a value which is two orders of magnitude smaller than the Km value corresponding to ATP utilization in poly(rAU) synthesis. Simple models are proposed which allow a comparison with E.coli RNA polymerase, for which the results are well documented.

Control of RNA polymerase binding to chromatin by variations in linker histone composition

We have measured the frequency of initiation sites in chromatin for RNA polymerase in vitro as a function of the composition of linker histones (H1 and its analogues). In linker histone-depleted chromatin, RNA chain initiation appears to be restricted to the exposed linker DNA. On titration with purified linker histones, initiation is further restricted to an extent determined by the amount and type of linker histone, and the source of depleted chromatin. The extent of repression is correlated with the capacity of linker histones to induce the formation of higher-order structure in the complex. The results suggest that the effects of linker histones are mediated through the higher-order structure of chromatin, which prevents access of polymerase to the linker DNA. Accordingly, we find that structures imposed by the linker histones after polymerase binding are not inhibitory. Microscopy reveals that the higher-order structure in partially condensed chromatin is discontinuous, with solenoidal units spaced by sections of unravelled nucleosomes. Since salt stimulation of linker histone exchange does not result in derepression of linkers in our assay, we conclude that the distribution of higher-order units in chromatin is static and that the linker histones exchange between high-affinity sites in established units. We have previously shown that the globin gene is selectively unfolded in tissues that express the gene. The present results suggest that the transcriptional activity of specific genes is maintained by differential linker histone binding within chromatin.

Enzymatic properties of plant RNA polymerases : An approach to the study of transcription in plants

Results obtained in the past few years in the study of the reaction mechanism of plant RNA polymerases are reviewed and discussed. They suggest that valuable information can be obtained using a highly simplified transcription system composed of purified plant enzymes and cloned genes. This type of approach may provide a starting point for the development of an in vitro transcription system. The detailed study of the fundamental enzymatic properties of the plant RNA polymerases allows a comparison with the well documented corresponding bacterial enzyme.

Complex RNA chain elongation kinetics by wheat germ RNA polymerase II

Kinetics of RNA chain elongation catalyzed by wheat germ RNA polymerase II have been studied using various synthetic DNA templates in the presence of excess dinucleotide monophosphate primers. With single- or double-stranded homopolymer templates, the double reciprocal plots 1/(velocity) as a function of 1/(nucleotide substrate) exhibit positive, negative or no curvature. With poly(dAT) as template, the mechanism of nucleoside monophosphate incorporation into RNA is not the ping-pong kinetic mechanism which was derived for E. coli RNA polymerase (6). Noncomplementary nucleoside triphosphates inhibit RNA transcription allosterically. Cordycepin triphosphate behaves as ATP, and not only inhibits AMP incorporation but also that of UMP and GMP on appropriate templates. The reason for this complex kinetic behavior is not yet understood. Possibilities are raised that there are several nucleoside triphosphate binding sites on wheat germ RNA polymerase II, that additional nucleoside triphosphate dependent enzymatic activities are required for reaction to occur or that the Km value for incorporation of a given nucleoside monophosphate into RNA is dependent on the length of the RNA chain and/or the nucleotide sequence surrounding the complementary base on the DNA template.

A topological model for chromatin transcription and a role for nucleosome linkers

There is a good deal of evidence that transcribing RNA polymerase may translocate across nucleosomes without their displacement and (or) rearrangement. A topological model for RNA chain elongation on a nucleosome is considered here. A new mechanism of RNA polymerase translocation is suggested in order to avoid the steric hindrances inherent in the model. It is shown that a transcribed nucleoprotein fiber should be interrupted by protein-free DNA stretches (nucleosome linkers) to allow release of nascent RNA. Possible verifications and consequences of the model are discussed.

The quaternary structure of Escherichia coli RNA polymerase studied with (scanning) transmission (immuno)electron microscopy

A model for the quaternary structure of Escherichia coli RNA polymerase (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6) is presented. It is based on results from classification of profiles of enzyme molecules, and from application of immuno electron microscopy. Classification of molecules, prepared with the single carbon layer technique, was first achieved for images recorded in dark field with the scanning transmission electron microscope and later on for images recorded in bright-field transmission electron microscopy. It results in five approximately equally sized groups, containing about 80% of the core enzyme profiles. Holoenzyme profiles can be grouped into the same classes, and have approximately the same dimensions (9 nm X 16 nm). Based on the shapes and sizes of the classified profiles, a tentative model for core enzyme has been constructed. Correlation of shadow projections of this model, with the distributions of attachment sites of antibodies against alpha, beta, beta' and sigma over the profiles, has led to models for core and holoenzyme in which the subunits are localized. The model is compared with literature data on the quaternary structure of RNA polymerase.