Enzymatic properties and cooperative effects in the kinetics of wheat-germ RNA polymerases. A comparative study of the three nuclear enzyme classes

Potential memory and hysteretic effects in transcription

Kinetic results of RNA-chain elongation catalysed by wheat-germ RNA polymerase II are analysed according to the concept that DNA-dependent conformational transitions of the transcription complex intervene during transcription. A model is presented, involving participation of several forms of the transcription complex with different catalytic properties, generated by the sequence and/or conformation of the DNA template and/or the experimental conditions. The available experimental data suggest that these forms are interconvertible. Examples in which hysteretic transitions might occur are outlined, such as termination of transcription and transition from abortive to productive elongation in the first steps of RNA synthesis. The slow catalytic adaptation of the transcription complex to the template sequence might be a more general phenomenon for enzyme systems acting on polynucleotide templates, in view of the recent proposal that enzyme memory effects may also have some importance in DNA replication and messenger RNA (mRNA) translation.

Kinetic co-operativity of wheat-germ RNA polymerase II with adenosine 5'-[beta gamma-imido]triphosphate as substrate

A kinetic study of productive RNA chain elongation indicates that adenosine 5'-[beta gamma-imido]triphosphate can serve as substrate in reactions catalysed by purified wheat-germ RNA polymerase II on a poly[d(A-T)] template. However, in contrast with the results obtained with the natural substrate ATP, the double-reciprocal plots, 1/velocity versus 1/[nucleotide], are not linear but characteristic of apparent negative co-operativity. The extent of the kinetic co-operativity is modified when the reactions are conducted in the additional presence of fixed amounts of an alternative substrate such as ATP or inhibitors such as dATP or cordycepin triphosphate. Analogous results are obtained whether the reactions are carried out in the presence of Mg2+ or Mn2+ as the metal ion cofactor. However, the data show that with Mn2+ the RNA polymerase is less specific in substrate recognition than with Mg2+. Tentative kinetic models are proposed to account for the rate measurements.

Effect of salts on abortive and productive elongation catalysed by wheat germ RNA polymerase II

Modification of the ionic conditions in reaction assays containing wheat germ RNA polymerase II and poly(dAT) as template markedly alters the catalytic properties of the transcription complexes. These effects have been studied by measuring the rate of abortive initiation and the extent of productive RNA synthesis. Using combinations of metal ions or various salts, a marked inhibition of abortive initiation was always associated with an increased length of RNA chains. These results are discussed in terms of modulation of the stability of transcription complexes induced by salts or divalent cations. The behavior exhibited by wheat germ RNA polymerase II is also discussed in comparison with previously reported results for procaryotic and eucaryotic RNA polymerases.

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.

Eukaryotic RNA polymerases

This review will attempt to cover the present information on the multiple forms of eukaryotic DNA-dependent RNA polymerases, both at the structural and functional level. Nuclear RNA polymerases constitute a group of three large multimeric enzymes, each with a different and complex subunit structure and distinct specificity. The review will include a detailed description of their molecular structure. The current approaches to elucidate subunit function via chemical modification, phosphorylation, enzyme reconstitution, immunological studies, and mutant analysis will be described. In vitro reconstituted systems are available for the accurate transcription of cloned genes coding for rRNA, tRNA, 5 SRNA, and mRNA. These systems will be described with special attention to the cellular factors required for specific transcription. A section on future prospects will address questions concerning the significance of the complex subunit structure of the nuclear enzymes; the organization and regulation of the gene coding for RNA polymerase subunits; the obtention of mutants affected at the level of factors, or RNA polymerases; the mechanism of template recognition by factors and RNA polymerase.

DNA-dependent RNA polymerase II from nuclei of suspension-cultured tobacco cells

From isolated nuclei of suspension cultured cells of Nicotiana tabacum. DNA-dependent RNA polymerase II (E.C. 2.7.76) has been purified to homogeneity as evidenced by polyacrylamidegel electrophoresis under non-denaturing conditions. The purified enzyme had a specific activity of more than 15 nmol min(-1)·mg(-1) with denatured calf thymus DNA as template. Sodium-dodecyl-sulfate gel electrophoresis and protein highperformance liquid chromatography revealed a subunit composition of four proteins with molecular weights of 165 000, 135 000, 35 000 and 25 000 and with a stoichiometry of 1:1:2:2. The RNA polymerase did not exhibit any detectable proteinkinase activity. The 25 000 subunit binds ADP in a molar ratio of 1:1; it could not be decided whether this subunit has an ATPase activity or is merely an acceptor of ADP.

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.

Selective transcription of a cloned cauliflower mosaic virus DNA fragment in vitro by soybean RNA polymerase II in the presence of dinucleotide primers

Transcription of a cloned cauliflower mosaic virus (CaMV) DNA fragment (plasmid pCa 8) was studied at a low enzyme: DNA ratio. Preincubation with purine nucleoside triphosphates leads to essentially random transcription, while in the presence of a dinucleoside monophosphate and a purine nucleoside triphosphate in the preincubation medium certain combinations prime preferential transcription of the eucaryotic moiety of the chimeric plasmid. Characterisation of transcription primed by the most efficient combination, ApG + ATP, shows that a low enzyme: DNA ratio is absolutely essential for selective initiation. Interestingly the presence of the eucaryotic insertion is essential for the transcription of vector sequences. Analysis of RNA primed by ApG + ATP and of short chains synthesised in the presence of the GTP analogue 3'-OMeGTP shows a high degree of selectivity of transcription initiation sites. Hybridisation of primed RNA to restriction fragments of pCa8 shows that initiation occurs within a limited region of the inserted CaMV fragment.