Thermodynamic studies of the interaction of alpha-chymotrypsin with water. I. Determination of the isosteric enthalpies and entropies of water binding to the native enzyme

RNA polymerase enzymes isolated from soybean hypocotyl tissue during successive developmental stages (2-8 days old) have been fractionated by Sephadex column isoelectric focusing. Both the enzymes bound to chromatin and those enzymes free in the soluble phase were investigated during development with respect to their distribution within these two pools. All observed activites were classified according to their alpha-amanitin sensitivity and isoelectric points. Two Class I subspecies (Ia, Ib) and two Class III subspecies (IIIa, IIIb) were continually present bound to chromatin throughout the developmental sequences except the IIb form which was absent at the latest stage. However, a great multiplicity (9 total) of Class II activities (totally inhibited by alpha-amanitin) were observed to be bound to chromatin at the 2nd day stage. These forms were first released from the chromatin complex and recovered in a soluble pool (4th day stage). Subsequent hypocotyl development was accompanied by the gradual disappearance of these Class II subspecies from this pool (6th day) until only two soluble species and one chromatin-bound Class II activity remained (8th day). These observations indicate that the early development of this tissue is accompanied by a dramatic alteration in the conplexity of chromatin-bound RNA polymerase subspecies. Such events may in part determine the domain of RNA secies synthesized at successive developmental stages.     

Effects of partial hepatectomy on RNA polymerase activities in mouse liver

Chromatin-bound and poly[d(A-T)]dependent RNA polymerase I plus III and II activities of mouse liver were analysed 24 and 48 hr after partial hepatectomy. Chromatin-bound RNA polymerase I plus III activity showed an increase of 57% at 24 hr and 51% at 48 hr after partial hepatectomy. There was a decrease in chromatin-bound RNA polymerase II activity of 15% at 24 hr and 34% at 48 hr after partial hepatectomy. There was no significant changes in poly[d(A-T)]dependent RNA polymerase activities. Heparin caused an approximately 10-fold increase in chromatin-bound RNA polymerase II activity. The stimulation by heparin was significantly increased 48 h after partial hepatectomy. Anaesthesia and/or surgery had great influence on RNA polymerase activities. At 24 hr after operation, chromatin-bound RNA polymerase I plus III and II activities were depressed, and the liver cell chromatin was more susceptible to stimulation by heparin.     

Viral RNA synthesis and levels of DNA-dependent RNA polymerases during replication of adenovirus 2.

The rates of RNA synthesis in cultured human KB cells infected by adenovirus 2 were estimated by measuring the endogenous RNA polymerase activities in isolated nuclei. The fungal toxin alpha-amanitin was used to determine the relative and absolute levels of RNA polymerases I, II, and III in nuclei isolated during the course of infection. Whereas the level of endogenous RNA polymerase I activity in nuclei from infected cells remained constant relative to the level in nuclei from mock-infected cells, the endogenous RNA polymerase II and III activities each increased about 10-fold. These increases in endogenous RNA polymerase activities were accompanied by concomitant increases in the rates of synthesis in isolated nuclei of viral mRNA precursor, which was quantitated by electrophoretic analysis on polyacrylamide gels. The cellular RNA polymerase levels were measured with exogenous templates after solubilization and chromatographic resolution of the enzymes on DEAE-Sephadex, using procedures in which no losses of activity were apparent. In contrast to the endogenous RNA polymerase activities in isolated nuclei, the cellular levels of the solubilized class I, II, and III RNA polymerases remained constant throughout the course of the infection. Furthermore, no differences were detected in the chromatographic properties of the RNA polymerases obtained from infected or control mock-infected cells. These observations suggest that the increases in endogenous RNA polymerase activities in isolated nuclei are not due to variations in the cellular concentrations of the enzymes. Instead, it is likely that the increased endogenous enzyme activities result from either the large amounts of viral DNA template available as a consequence of viral replication of from replication or from functional modifications of the RNA polymerases or from a combination of these effects.     

Viral RNA Synthesis and Levels of DNA-Dependent RNA Polymerases During Replication of Adenovirus 2

The rates of RNA synthesis in cultured human KB cells infected by adenovirus 2 were estimated by measuring the endogenous RNA polymerase activities in isolated nuclei. The fungal toxin α-amanitin was used to determine the relative and absolute levels of RNA synthesis by RNA polymerases I, II, and III in nuclei isolated during the course of infection. Whereas the level of endogenous RNA polymerase I activity in nuclei from infected cells remained constant relative to the level in nuclei from mock-infected cells, the endogenous RNA polymerase II and III activities each increased about 10-fold. These increases in endogenous RNA polymerase activities were accompanied by concomitant increases in the rates of synthesis in isolated nuclei of viral mRNA precursor, which was monitored by hybridization to viral DNA, and of viral 5.5S RNA, which was quantitated by electrophoretic analysis on polyacrylamide gels. The cellular RNA polymerase levels were measured with exogenous templates after solubilization and chromatographic resolution of the enzymes on DEAE-Sephadex, using procedures in which no losses of activity were apparent. In contrast to the endogenous RNA polymerase activities in isolated nuclei, the cellular levels of the solubilized class I, II, and III RNA polymerases remained constant throughout the course of the infection. Furthermore, no differences were detected in the chromatographic properties of the RNA polymerases obtained from infected or control mock-infected cells. These observations suggest that the increases in endogenous RNA polymerase activities in isolated nuclei are not due to variations in the cellular concentrations of the enzymes. Instead, it is likely that the increased endogenous enzyme activities result from either the large amounts of viral DNA template available as a consequence of viral replication or from functional modifications of the RNA polymerases or from a combination of these effects.     

Multiple forms of DNA-dependent RNA polymerases in Xenopus laevis. Rapid purification and structural and immunological properties

DNA-dependent RNA polymerases I, II, and III (EC 2.7.7.6) were isolated from Xenopus laevis ovaries. The soluble enzymes were precipitated with polyethyleneimine and subjected to chromatography on heparin-Sepharose, DEAE-Sephadex, and phosphocellulose. RNA polymerase I was subjected to an additional chromatographic step on CM-Sephadex. The procedure required 40 h and produced purified RNA polymerase forms IA, IIA, and III in yields of 5 to 40%. The specific activities of RNA polymerases IIA and III (on native DNA) were comparable to those reported from other eukaryotic sources, whereas that of form IA was severalfold greater than the specific activities reported for other purified class I RNA polymerases. The complex subunit compositions of chromatographically purified RNA polymerases IA, IIA, and III were distinct when analyzed by polyacrylamide gradient gel electrophoresis under denaturing conditions, although all three classes contained polypeptides with Mr = 29,000, 23,000, and 19,000. Antibodies prepared against RNA polymerase III showed common antigenic determinants within the class I, II, and III enzymes. The sites responsible for the cross-reaction are located, at least in part, on the common 29,000-dalton polypeptide.     

Changes in the content of cyclic AMP and cyclic GMP during the development of Xenopus laevis.

The levels of the three major DNA-dependent RNA polymerases (enzymes I, II and III) present in the dimorphic fungus Mucor rouxii have been investigated during the transition from yeast-like cells to mycelial growth. Increases in the specific activity of crude extracts were observed at 2 h and at 6 h after induction of mycelium formation by aeration of yeast-like cells. These increases could be attributed to changes in the specific activities of enzymes I and II. Alterations were also found in the relative amounts of enzymes I and II: prior to aeration, 31% of the total polymerase activity of crude extracts was present as enzyme I; after 2 h of aeration, the specific activity of this enzyme doubled and the relative amount increased to 64% of the total activity. After 6 h of aeration, the relative amounts of enzymes I and II were 25 and 65%, respectively, and the specific activity of enzyme II had nearly doubled. The amounts and specific activities of enzyme III did not change significantly during the transition.     

Comparison of the effects of polyamines on the activities of RNA polymerases from murine normal tissues and transplantable tumors

Nuclear DNA-dependent RNA polymerases I, II and III were purified from kidney, liver and spleen from Swiss mice (Mus musculis) and from seven transplantable murine tumors. In the presence of the optimal concentration of (NH4)2SO4 for each polymerase, 1-8 mM spermidine or spermine stimulated most polymerases several fold, and generally, enzyme I was stimulated more than either enzyme II or III. Spermine was more efficacious than spermidine as a stimulant of polymerase activity except for polymerase III from three tumors. Tumor polymerases I (or II) and the corresponding normal tissue enzymes responded similarly to the polyamines. Stimulation of a RNA polymerase by a polyamine could not be correlated with the growth rate of the tissues of polymerase origin or with the tissue's RNA polymerase or RNA synthetic activities.     

Mouse Brain DNA-Dependent RNA Polymerases After Chronic Morphine Treatment

Abstract: Chronic morphine pellet implantation was found to decrease the specific activity of two forms of mouse brain RNA polymerase I and to alter the requirements of Mg²⁺ and Mn²⁺ for the activities of RNA polymerases II and III. DNA-dependent RNA polymerases were partially purified from small dense nuclei isolated from brains of naive and morphine tolerant-dependent mice, and three RNA polymerases were separated on a DEAE-Sephadex A-25 column. The three fractions, referred to as peak I, peak II, and peak III, were studied, characterized, and identified as being RNA polymerases I, II, and III, respectively. Chronic-morphine pellet implantation resulted in a lower specific activity of RNA polymerase I, but the specific activities of RNA polymerases II and III were not affected. This effect was prevented by preimplantation of a naloxone pellet and thus was narcotic-specific. Chronic morphine treatment lowered the concentration of Mg²⁺ required for optimal activity of RNA polymerase II and elevated the Mn²⁺-Mg²⁺ activity ratios of RNA polymerases II and III. A second DEAE-Sephadex A-25 column chromatography of the peak I RNA polymerase was carried out, revealing five component activity peaks. Two of these contained lower specific activities as a result of chronic morphine pelletimplantation. These specific changes in RNA polymerase function in morphine tolerance-dependence may be associated with the elevated chromatin template activities, altered chromatin phosphorylation, and elevated rates of cell-free translation that have been reported by others.     

A simple solubilization method for loosely and tightly chromatin-bound RNA polymerase II from rat liver nuclei

Rat liver chromatin-bound RNA polymerase II could be differentially solubilized into two distinct populations, loosely and tightly bound enzymes, by a simple method. By this method the recovery of the solubilized enzyme from the chromatin fraction could be increased considerably as compared with the procedure of Yu (1). The two chromatin-bound enzymes had different properties:

1. Loosely bound enzyme was easily extractable from chromatin with relatively mild ionic condition (0.5 M NaCl); the tightly bound enzyme had to be solubilized by more drastic conditions such as sonication or nuclease treatment.
2. Loosely bound enzyme could not efficiently transcribe the chromatin template, but the tightly bound enzyme was active toward the same template. The latter enzyme is involved in the tight complex with the RNA synthesis activating factors.
3. Cycloheximide treatment in vivo suggests that the two enzymes have different turn-over rates.

Therefore, with this simple solubilization method the functionally different two chromatin-bound RNA polymerase II activities can be estimated.     

Three distinct forms of DNA-dependent RNA polymerase III from kidney

DNA-dependent RNA polymerases were extracted from nuclei isolated from 1 kg of pig kidney and subjected to DEAE-Sephadex chromatography using a step-wise salt gradient. Fractions corresponding to RNA polymerase III were pooled and rechromatographed on a second DEAE-Sephadex column using a linear salt gradient. At least three distinct peaks, designated as IIIA, IIIB, and IIIC were resolved. These peaks exhibited α-amanitin dose response curves characteristic of RNA polymerase III. Detection of the enzyme was facilitated by assaying with either highly polymerized calf thymus DNA and spermine or with poly [d(A-T)]. The heterogeneity of this enzyme became even more pronounced after further purification. Under the same conditions, both RNA polymerases I and II were resolved at most to two subspecies. The highly heterogeneous nature of RNA polymerase III is consistent with the large number of RNA species believed to be synthesized by this enzyme class.     

Differential changes of tightly chromatin-bound RNA polymerase II in starved and cycloheximide-treated rat liver nuclei

In order to investigate the physiological function of loosely and tightly chromatin-bound RNA polymerase IIin vivo (1), the changes of these enzyme activities in cycloheximide-treated or starved rat liver nuclei were studied. Total nuclear mRNA synthesis activity in starved rats was considerably decreased, but that of cycloheximide-treated rats was not affected significantly. In starved rats, tightly bound enzyme activity was much more repressed as compared with that of loosely bound enzyme. On the other hand, cycloheximidetreated rats showed the reverse relationship. Thus, mRNA synthesis activity in hepatic nuclei seems to be dependent on the tightly bound RNA polymerase II activity. However, the difference of nuclear mRNA synthesis in both cases can not be explained by the change of chromatin-bound enzyme activity of Yu (2).     

RNA polymerase activities and chromatin protein composition of rat liver during methionine deprivation and refeeding

The reversible effect of dietary methionine deficiency was studied in young adult rats. The sensitivity of nuclear chromatin to micrococcal nuclease (EC3.1.4.7) digestion and the composition of the chromatin proteins were unaffected by the dietary regimens. The specific chromatin-bound RNA polymerase II activity decreased during methionine deficiency. Refeeding of methionine for 2 days restored the activity in the nuclease-released chromatin. RNA polymerase I plus III activity remained unchanged. Total RNA polymerase activity changed with the liver wet weight which was reduced during methionine deficiency and was not restored to control level after 2 days of methionine refeeding. RNA polymerase activity was altered by methionine deficiency. The recovery was independent of major modifications of the chromatin structure and protein composition.     

Effect of 3-methylcholanthrene administration on hepatic ribonucleic acid polymerase activities

The effect of the in vivo administration of 3-methylcholanthrene upon rat hepatic RNA polymerase activities was investigated. Aggregrate RNA polymerase activity assayed in liver nuclei was stimulated by 33% over control. Characterization of the individual RNA polymerase activities by virtue of their differential sensitivity to α-amanitin revealed that RNA polymerase I activity was maximally increased by 70% at approx. 16 h post-administration of the polycyclic hydrocarbon; RNA polymerase II activity was stimulated by 33%. The kinetics of RNA polymerases I and II stimulation differed in that the nucleolar enzyme's activity increased earlier and peaked later. RNA polymerase III activity was not significantly different from control. Phenobarbital, another inducer of the mixed function oxidases, had essentially no effect on the activity of hepatic RNA polymerases. Solubilization of the RNA polymerases followed by separation on diethylaminoethyl (DEAE)-Sephadex allowed for a comparison of the treated and control enzymatic activities using a common exogenous template. While no qualitative difference was evident, RNA polymerases I and II isolated from 3-methylcholanthrene-treated rats again were more active than control, indicating an effect of the polycyclic hydrocarbon at the level of the enzyme.     

The thrombin-like enzyme from Bothrops atrox snake venom. Properties of the enzyme purified by affinity chromatography on p-aminobenzamidine-substituted agarose.

The trhombin-like activities from the snake venoms of two subspecies of Bothrops atrox, moojeni (type I) and marajoensis (type II), were purified to homogeneity by affinity chromatography on a support consisting of the inhibitor, p-aminobenzamidine, linked to Sepharose 4B with a spacer of diaminodipropylaminosuccinate. At room temperature the enzyme was not bound to the affinity support but rather was retarded in relation to the unbound protein. As a result the thrombin-like activity eluted in a large volume following the main protein fraction. However, at 4 degrees the enzyme was absorbed to the affinity support and could be eluted specifically with the ligand benzamidine (0.15 M). Optimal conditions for column loading and washing were 0.05 M Tris.HCl/0.4 M NaCl, pH 9.0 at 4 degrees. The type I enzyme isolated in this manner showed a single major band on pH 8.9 disc gel electrophoresis as well as two minor bands. Further purification by isoelectric focusing yielded one major and two minor components. All three protein fractions had identical thrombin-like activities and amino acid composition. The major band had a specific activity of 210 to 230 NIH thrombin units/mg, a S20, w of 2.65 S, a molecular weight of 29,000, and an E1% 280 of 15.6. This protein has a carbohydrate content, measured as hexose, glucosamine, and sialic acid, of 27%. From the amino acid and carbohydrate composition a partial specific volume of 0.700 ml/g was calculated. The type I enzyme, purified on affinity chromatography only, did not activate Factor XIII and was free of thromboplastin-like activity. The type II enzyme behaved very differently from the type I on pH 8.9 polyacrylamide disc gels yielding two major bands and two minor bands. The relative amounts of these four bands were not a function of purity. The type II enzyme had a specific activity of 650 to 700 NIH thrombin units/mg, a S20, w of 2.60, and a molecular weight of 31,400.     

Large scale isolation of RNA polymerase I of Tetrahymena pyriformis and the identification of polymerase-associated polypeptides

A procedure has been developed for a large scale and rapid isolation of RNA polymerase I (EC 2.7.7.6) of Tetrahymena pyriformis. The enzyme is precipitated from the cell homogenate by Polymin P, extracted from the sediment and separated from RNA polymerase II by a treatment with phosphocellulose. The further purification procedure involves sedimentation in glycerol gradients and chromatography on heparin-Sepharose and DEAE-Sephadex. The last step achieved the separation of RNA polymerase I from RNA polymerase III. On the basis of different criteria RNA polymerase I is assumed to consist of two large subunits of 180 and 118 kDa and nine subunits smaller than 50 kDa. Additional polypeptides have been identified which are associated with RNA polymerase I but are not found in integral stoichiometric amounts. Except for certain minor differences RNA polymerase I purified from the cell homogenate shows the same structure as the enzyme obtained from isolated macronuclei (Mueller et al., 1985).