Nucleolar DNA-dependent RNA polymerase from rat liver. 2. Two forms and their physiological significance

The Mammalian and Yeast A49 and A34 Heterodimers: Homologous but Not the Same

Ribosomal RNA synthesis is the rate-limiting step in ribosome biogenesis. In eukaryotes, RNA polymerase I (Pol I) is responsible for transcribing the ribosomal DNA genes that reside in the nucleolus. Aberrations in Pol I activity have been linked to the development of multiple cancers and other genetic diseases. Therefore, it is key that we understand the mechanisms of Pol I transcription. Recent studies have demonstrated that there are many differences between Pol I transcription in yeast and mammals. Our goal is to highlight the similarities and differences between the polymerase-associated factors (PAFs) in yeast and mammalian cells. We focus on the PAF heterodimer A49/34 in yeast and PAF53/49 in mammals. Recent studies have demonstrated that while the structures between the yeast and mammalian orthologs are very similar, they may function differently during Pol I transcription, and their patterns of regulation are different.

Multiple protein-protein interactions by RNA polymerase I-associated factor PAF49 and role of PAF49 in rRNA transcription

We previously demonstrated the critical role of RNA polymerase I (Pol I)-associated factor PAF53 in mammalian rRNA transcription. Here, we report the isolation and characterization of another Pol I-associated factor, PAF49. Mouse PAF49 shows striking homology to the human nucleolar protein ASE-1, so that they are considered orthologues. PAF49 and PAF53 were copurified with a subpopulation of Pol I during purification from cell extracts. Physical association of PAF49 with Pol I was confirmed by a coimmunoprecipitation assay. PAF49 was shown to interact with PAF53 through its N-terminal segment. This region of PAF49 also served as the target for TAF(I)48, the 48-kDa subunit of selectivity factor SL1. Concomitant with this interaction, the other components of SL1 also coimmunoprecipitated with PAF49. Specific transcription from the mouse rRNA promoter in vitro was severely impaired by anti-PAF49 antibody, which was overcome by addition of recombinant PAF49 protein. Moreover, overexpression of a deletion mutant of PAF49 significantly reduced pre-rRNA synthesis in vivo. Immunolocalization analysis revealed that PAF49 accumulated in the nucleolus of growing cells but dispersed to nucleoplasm in growth-arrested cells. These results strongly suggest that PAF49/ASE-1 plays an important role in rRNA transcription.

At the crossroads of growth control; making ribosomal RNA

Although the mechanisms of cell cycle control are well established, the factors controlling cell growth and target size are still poorly understood. Much evidence suggests that ribosome biogenesis, and in particular the synthesis of the rRNAs, plays a central role not only in permitting growth, but also in regulating it. In the past few years we have begun to penetrate the network linking rRNA gene transcription to growth.

hRRN3 is essential in the SL1-mediated recruitment of RNA Polymerase I to rRNA gene promoters

A crucial step in transcription is the recruitment of RNA polymerase to promoters. In the transcription of human rRNA genes by RNA Polymerase I (Pol I), transcription factor SL1 has a role as the essential core promoter binding factor. Little is known about the mechanism by which Pol I is recruited. We provide evidence for an essential role for hRRN3, the human homologue of a yeast Pol I transcription factor, in this process. We find that whereas the bulk of human Pol I complexes (I alpha) are transcriptionally inactive, hRRN3 defines a distinct subpopulation of Pol I complexes (I beta) that supports specific initiation of transcription. Human RRN3 interacts directly with TAF(I)110 and TAF(I)63 of promoter-selectivity factor SL1. Blocking this connection prevents recruitment of Pol I beta to the rDNA promoter. Furthermore, hRRN3 can be found in transcriptionally autonomous Pol I holoenzyme complexes. We conclude that hRRN3 functions to recruit initiation-competent Pol I to rRNA gene promoters. The essential role for hRRN3 in linking Pol I to SL1 suggests a mechanism for growth control of Pol I transcription.

Estrogen-induced changes in rRNA accumulation and RNA polymerase I activity in the rat pituitary: correlation with pituitary tumor susceptibility

Chronic treatment with the synthetic estrogen diethylstilbestrol induces pituitary tumors in rats and the susceptibility to such tumors is highly strain dependent. The Fischer 344 (F344) strain, which is particularly susceptible, develops pituitary tumors after 30-55 days of estrogen treatment. In contrast, the Sprague-Dawley (SD) strain is relatively resistant to such tumors. DES implants (5 mg) were placed in 21-day-old male rats over a 10-day period and changes in their testes and pituitaries were monitored. Both F344 and SD strains responded similarly by exhibiting a measurable decrease in testes weight to one-third that of controls on day 10. In F344 rats, DNA synthesis in the pituitary increased to 228% as compared with controls after 3 days of DES treatment and remained high on days 7 and 10. In SD rats, DNA synthesis increased to only 150% of that exhibited by controls on day 3 and started to decline on day 7. Surprisingly, total RNA accumulation also responded to DES differentially between these two strains. In F344 rats, the RNA level was 250% as compared with that of controls after 3 days of DES treatment and continued to increase gradually on days 7 and 10. The RNA level in the SD strain increased only slightly from the same DES treatment. A nuclear run-on assay showed elevated pituitary transcription of ribosomal DNA in the F344 rats after 3 days of estrogen administration. The enzymatic activity of pituitary RNA polymerase I, the enzyme responsible for initiating rRNA synthesis, increased twofold in F344 rats when measured after 3 days of estrogen treatment whereas no increase was observed in the SD rats. These results suggest that estrogen-induced changes in the accumulation of rRNA occur at a very early stage in tumorigenesis, prior to any visible tumor growth in the rat pituitary.

Activated ribosomal RNA synthesis in regenerated rat liver upon inhibition of protein synthesis

Cycloheximide (Cyh), administered at a dose of 5 mg/kg body wt blocks protein synthesis in normal rat liver (NRL) and regenerating rat liver (RRL). The rate of synthesis of 45S pre-rRNA in RRL, studied after RNA labelling in vivo is activated 2.8 times. Pre-r RNA synthesis in RRL is more sensitive to the stopped translation, but never falls down to the level in NRL. The major contribution to the rDNA transcription activation in RRL comes from the 20-fold increase in the number of pol I molecules engaged in the transcription, the elongation rate being 1.4-fold accelerated. Cyh quenches partially the enhanced rDNA transcription in RRL: the number of pol I molecules and their elongation rate are about 1.7-fold and 1.5-fold higher, respectively, than the corresponding values in NRL after Cyh treatment. The results show that two different mechanisms control the number and the rate of initiation and elongation of RNA polymerase I in rat liver; one of them depends on continuous protein synthesis and can be inactivated by Cyh, the other is Cyh resistant.

Isolation, fractionation and reconstitution of a nuclear extract capable of transcribing ribosomal DNA

A procedure for preparing a nuclear extract that efficiently transcribes rat rDNA in vitro has been developed. This procedure, which is based on the protocol described by Dignam et al. (Nucl Acids Res 11:1475, 1983), allows the preparation of extract from large or small amounts of material and requires neither ultracentrifugation nor column chromatography. These extracts were found to be more efficient than other transcription systems. Extract prepared as described routinely synthesize 1-2 transcripts per linear template, and could synthesize upto 6 transcripts per linear template at an elongation rate of 2.1 nucleotides per second. 0.3 M NaCl extracts of nuclei contained RNA polymerase I, but did not transcribe rat rDNA in vitro, whereas extract prepared with 0.42 M NaCl did. The 0.42 M NaCl extract of nuclei was fractionated by chromatography on DEAE-Sephadex and heparin-Sepharose. Two activities were identified that were required for accurate in vitro transcription by endogenous RNA polymerase I. One of these activities was required for accurate initiation, and the second inhibited non-specific transcription. The fraction required for accurate initiation by the endogenous RNA polymerase I is that factor which directs species specific transcription, as it also directed the transcription of rat rDNA by nuclear extracts of HeLa cells. Combining that same chromatographic fraction of the 0.42 M NaCl extract with the 0.3 M NaCl extract resulted in specific transcription. These results suggest that a fraction of the RNA polymerase I molecules may exist in a complex with some, or all, of the factors required for transcription.

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.

Aurintricarboxilic acid as a tool for investigating the template-bound and unbound forms of RNA polymerase I in permeabilized cells

The presence of template-bound and unbound RNA polymerase I in permeabilized cells was investigated. The two enzyme forms were defined on the basis of their different susceptibilities towards aurintricarboxilic acid (ATA). It was found that addition of ATA to permeabilized cells suppresses initiation of new RNA chains by RNA polymerase I but has no effect on the activity of the enzyme already engaged in transcription. This last activity is not affected even after washing the permeabilized cells for removal of the ATA. The RNA polymerase I activity solubilized from permeabilized cells pre-treated with ATA is 60-70% of that obtained from non-treated controls. The decrease of the solubilized enzyme activity was observed after purification of the enzymes by DEAE-Sephadex columns and cannot be attributed to the presence of inhibitory or activating factors in the enzyme preparations. The simplest interpretation of these findings is that two distinct RNA polymerase I fractions, showing different sensitivities towards ATA are present in permeabilized cells. These fractions should represent the template-bound and unbound RNA polymerase I. The results also show that the amount of ATA-insensitive activity is lower in nuclei than in permeabilized cells, suggesting that detachment of template-bound enzyme occurs during nuclei isolation.

Posttranslationally modified ornithine decarboxylase may regulate RNA polymerase I activity

Purified ornithine decarboxylase (EC 4.1.1.17, ODC) transamidated with four putrescine moieties on four glutamine residues through the action of transglutaminase (EC 2.3.2.13, TGase) purified from guinea pig liver, when added to isolated rat liver nuclei, stoichiometrically increased the activity of RNA polymerase I (EC 2.7.7.6). The increase was relative to the pmoles of purified conjugated ODC added to the reaction and could be reinitiated after the reaction had plateaued by the further addition of ODC-putrescine conjugate. The kinetics of the reaction suggest that the ODC-putrescine conjugate was not reused but degraded after each initiation. Otherwise, the rapid plateau would not be observed. The repeated addition of 278 pmoles of purified ODC-putrescine conjugate to rat liver nuclear preparations containing 200 micrograms total protein consistently stimulated the incorporation of 600-700 pmoles UMP/mg protein. We suggest that ODC transamidated by its product putrescine may be the posttranslationally modified 65,000 Mr protein which has been reported by several laboratories to serve as a labile subunit of RNA polymerase I.

Glucocorticoids directly affect the synthesis of ribosomal RNA in rat-liver cells

Administration of the glucocorticoid dexamethasone to rats significantly stimulated the synthesis of ribosomal RNA by hepatic nuclei in vitro, as determined by hybridization to plasmid DNA containing the appropriate gene from X. laevis. This effect was also seen in rats in which RNA polymerase B had previously been blocked by the administration of alpha-amanitin. RNA synthesized in response to the hormone hybridized to both the 5' and 3' end of the gene for the precursor to ribosomal RNA. We conclude from these data that the steroid directly affects transcription of the ribosomal gene without obligatory participation of RNA polymerase B and hence the intermittent production of mRNA or its translation products.

Influence of 3-methylcholanthrene on liver nucleolar and nucleoplasmic activities of protein kinases and RNA polymerases

The experiments were designed to investigate some details of the action of 3-methylcholanthrene (3-MC) on the regulation of transcription. After a single intraperitoneal dose of 3-MC a significant increase in the activities of both nucleolar and nucleoplasmic protein kinases in hepatic cells of young rats was found. The maximal stimulation took place 24 hr after the administration of 3-MC and the extent of activation was much greater in the nucleolar fraction. There is a significant elevation of the activities of both functional forms, free and template-engaged, of RNA polymerase A 24 hr after a single injection of 3-MC. Free and engaged forms of extranucleolar RNA polymerase B show a different behaviour: after 24 hr of 3-MC administration the engaged form is markedly enhanced while the activity of the free enzyme shows a significant decrease. The more moderate increase in total RNA polymerase B activity is obviously preceded by a transfer of the enzyme from 'free' to 'engaged' form. Since the enhancement of protein kinase activities was accompanied by the stimulation of nuclear RNA polymerases we suggest that both kinds of enzymes are involved in an epigenetic mechanism of the inducing action of 3-MC on cytochrome P1-450.

Further characterization of the effects of 3-methylcholanthrene administration upon hepatic ribonucleic acid polymerase activities

The administration of 3-methylcholanthrene (MC) to rats results in a marked increase in the specific activities of hepatic RNA polymerases I and II. In the present study, we were able to show that this increase was not caused by a shift in the ratio of 'free' to 'template-engaged' RNA polymerase. By means of binding studies with [3H]amatoxin, we were unable to demonstrate any increase in the number of RNA polymerase II molecules in liver after MC administration to the rats. RNA polymerase I was purified in excess of 3000-fold from hepatic nuclei isolated both from control and MC-treated rats. The stimulation in activity was demonstrated at each step in the purification scheme until glycerol sedimentation analysis. Results from cation-exchange chromatography on phosphocellulose indicated that the polycyclic hydrocarbon increased the enzyme activity of RNA polymerase Ib somewhat specifically. Subsequent to glycerol gradient centrifugation, this stimulatory advantage was no longer evident. Reconstitution experiments revealed the presence of a stimulatory component, which was demonstrated in low molecular weight fractions from both control and experimental preparations.

Transcriptionally active RNA polymerases from Morris hepatomas and rat liver. Elucidation of the mechanism for the preferential increase in the tumour RNA polymerase I

The amount and/or activity of DNA-dependent RNA polymerase I, Ii and III from resting liver, regenerating liver and a series of Morris hepatomas (5123D, 7800, 7777, 3924A) were determined after extraction of the enzymes from whole tissue homogenates and subsequent fractionation by DEAE-Sephadex column chromatography. When compared with resting liver, the tumours exhibited a characteristic enzyme pattern in which polymerase I, but not II, was increased. The increase in RNA polymerase I was proportional to the tumour growth rates. Alterations in polymerase III were confined to the most rapidly proliferating hepatomas. By contrast, all classes of RNA polymerase were found to be increased during liver regeneration. Relative to resting liver, the fastest growing tumour, 3924A, exhibited the highest activities and/or amounts of RNA polymerase I (8-fold) and III (5-fold) per g of tissue. These alterations in the tumour RNA polymerases were reflected in corresponding increases in the transcriptionally active (bound or chromatin-associated) enzyme population. The mechanisms underlying the augmented synthesis of RNA in vitro by bound polymerase I from hepatoma 3924A were elucidated by product analysis. The results indicated that, relative to liver RNA polymerase I, the tumour enzyme produced more nascent RNA chains and elongated these chains at a faster rate. The number of 3'-termini, as measured by incorporation into uridine, was higher in the hepatoma even under conditions which prevented re-initiation. suggesting increased amount of transcriptionally active RNA polymerase I in the tumour.

Evidence for the existence of two forms of RNA polymerases I and II in insect wing epidermis

DNA-dependent RNA polymerases were solubilized from developing wings of the oak silkmoth, Antheraea pernyi, and partially purified by ion-exchange chromatography and sucrose gradient sedimentation. Four enzyme species were resolved on the basis of chromatographic behavior, divalent cation requirements, ionic strength optima, template preference and alpha-amanitin sensitivity. Each class (i.e. RNA polymerase I and II) was present in two forms termed IA, IB and IIA, IIB on the basis of their elution pattern from the column. Both class I enzymes were sensitive to high concentrations of alpha-amanitin but this may be due to general toxicity rather than specific inhibition. The intraclass variants did not differ significantly in enzymatic properties although form IIB was more sensitive to alpha-amanitin (50% inhibition at 2 . 10(-9) M) than form IIA (3 . 10(-8)M).

Isolation and characterization of RNA polymerase B from the larval fat body of the tobacco hornworm, Manduca sexta

DNA-dependent RNA polymerase B has been extensively purified from the larval fat body of the tobacco hornworm (Manduca sexta) by employing chromatography on ion-exchange columns of DEAE-Sephadex, DEAE-cellulose and phosphocellulose and centrifugation on glycerol gradients. The isolated enzyme after electrophoresis on acrylamide gels shows one main band and one minor band, both having enzyme activity sensitive to alpha-amanitin. The catalytic and physicochemical properties of the enzyme are similar to those of other eucaryotic B-type RNA polymerases. The enzyme has an apparent molecular weight of 530000, is inhibited 50% by alpha-amanitin at 0.04 microgram/ml and shows maximum activity on denatured DNA at 5 mM Mn2+ and 100 mM ammonium sulfate. An antibody was obtained that cross-reacts with the pure enzyme and forms a precipitin line. This antibody does not cross react with either Escherichia coli RNA polymerase or with wheat germ RNA polymerase but does react with one of the B polymerases isolated from wing tissue of the silkmoth, Antheraea pernyi.

Nucleolar DNA-dependent RNA polymerase from rat liver. 1. Purification and subunit structure

DNA-dependent RNA polymerase I (or A) was purified from rat liver nucleoli. DNA was effectively removed from the solubilized enzyme with a defined concentration of polyethyleneglycol. The enzyme was purified further with successive DEAE-Sephadex and phosphocellulose column chromatography followed by glycerol gradient centrifugation. The procedure yielded an electrophoretically homogeneous enzyme with a specific activity 400 times that of the nucleolar extracts. The recovery of the activity was approximately 20%. The RNA polymerase I eluted as a single peak from DEAE-Sephadex was separated into two distinct peaks by a phosphocellulose column. The first peak eluting at about 0.12 M ammonium sulfate was designated as RNA polymerase IA and the second peak eluting at about 0.18 M as RNA polymerase IB. In normal rat liver nucleoli IA enzyme comprised approximately 20% of the total RNA polymerase I activity and the IB enzyme comprised approximately 80%. On sodium dodecyl sulfate polyacrylamide gel electrophoresis, enzyme IB contained five subunits with molecular weights of 195000 (a), 130000 (b), 65000 (c), 40000 (d), and 19000 (e) at nearly equimolar amounts. The calculated molecular weight of the enzyme (449000) agreed well with that predicted from the sedimentation coefficient of the enzyme. Enzyme IA contained identical subunits except that subunit c was absent. Preliminary studies could not demonstrate any significant differences in template specificity between IA and IB enzyme.