Studies of the DNA helicase-RNA primase unit from bacteriophage T4. A trinucleotide sequence on the DNA template starts RNA primer synthesis

The purified DNA replication proteins encoded by genes 41 and 61 of bacteriophage T4 catalyze efficient RNA primer synthesis on a single-stranded DNA template. In the presence of additional T4 replication proteins, we demonstrate that the template sequences 5'-GTT-3' and 5'-GCT-3' serve as necessary and sufficient signals for RNA primer-dependent initiation of new DNA chains. These chains start with primers that have the sequences pppApCpNpNpN and pppGpCpNpNpN, where N can be any one of the four ribonucleotides. Each primer is initiated from the T (A-start primers) or C (G-start primers) in the center of the recognized template sequence. A subset of the DNA chain starts is observed when one of the four ribonucleoside triphosphates used as the substrates for primer synthesis is omitted; the starts observed reveal that both pentaribonucleotide and tetraribonucleotide primers can be used for efficient initiation of new DNA chains, whereas primers that are only 3 nucleotides long are inactive. It was known previously that, when 61 protein is present in catalytic amounts, the 41 and 61 proteins are both required for observing RNA primer synthesis. However, by raising the concentration of the 61 protein to a much higher level, a substantial amount of RNA-primed DNA synthesis is obtained in the absence of 41 protein. The DNA chains made are initiated by primers that seem to be identical to those made when both 41 and 61 proteins are present; however, only those template sites containing the 5'-GCT-3' sequence are utilized. The 61 protein is, therefore, the RNA primase, whereas the 41 protein should be viewed as a DNA helicase that is required (presumably via a 41/61 complex) for efficient primase recognition of both the 5'-GCT-3' and 5'-GTT-3' DNA template sequences.     

A novel in vitro replication system for Dengue virus. Initiation of RNA synthesis at the 3'-end of exogenous viral RNA templates requires 5'- and 3'-terminal complementary sequence motifs of the viral RNA

Positive strand viral replicases are membrane-bound complexes of viral and host proteins. The mechanism of viral replication and the role of host proteins are not well understood. To understand this mechanism, a viral replicase assay that utilizes extracts from dengue virus-infected mosquito (C6/36) cells and exogenous viral RNA templates is reported in this study. The 5'- and 3'-terminal regions (TR) of the template RNAs contain the conserved elements including the complementary (cyclization) motifs and stem-loop structures. RNA synthesis in vitro requires both 5'- and 3'-TR present in the same template molecule or when the 5'-TR RNA was added in trans to the 3'-untranslated region (UTR) RNA. However, the 3'-UTR RNA alone is not active. RNA synthesis occurs by elongation of the 3'-end of the template RNA to yield predominantly a double-stranded hairpin-like RNA product, twice the size of the template RNA. These results suggest that an interaction between 5'- and 3'-TR of the viral RNA that modulates the 3'-UTR RNA structure is required for RNA synthesis by the viral replicase. The complementary cyclization motifs of the viral genome also seem to play an important role in this interaction.     

Mode of inhibition of DNA synthesis induced by adenosine diphosphoribosylation of nuclear protein

DNA obtained after complete removal of the proteins from NAD-treated rat liver chromatin possessed template capacity equivalent to that obtained from untreated chromatin. The stepwise extraction of proteins from chromatin affected a gradual removal of labeled ADPR and a parallel decrease of the inhibition. The results of the present study suggest that the inhibition of the template capacity for DNA synthesis following preincubation of chromatin with NAD is dependent upon ADP-ribosylation of the associated proteins. The template capacity of chromatin and nucleoprotein complex (Weiss preparation) for DNA synthesis was inhibited, whereas the capacity for RNA synthesis was apparently not affected.     

Requirements and functions of vesicular stomatitis virus L and NS proteins in the transcription process in vitro

The L and NS proteins of vesicular stomatitis virus were purified from transcribing ribonucleoprotein complex and were used to study their requirements and functions during reconstitution of RNA synthesis in vitro. The requirements for L and NS proteins for optimal RNA synthesis were found to be catalytic and stoichiometric, respectively. Addition of increasing amounts of NS protein to N-RNA template and saturating L protein, the ratio of N-mRNA to leader RNA synthesis increased linearly. In contrast, when the concentration of L protein was increased the corresponding ratio remained constant. These results, coupled with the observation that the L protein is involved in the initiation of RNA synthesis, suggest that the NS protein is involved in the RNA chain elongation step. The NS protein possibly interacts with both the L protein and the template N-RNA and unwinds the latter to facilitate the movement of L protein on the template RNA.     

Changes in chromatin of Daucus carota cells during embryogenesis

Cells of carrot (Daucus carota var. Rote Riesen) were cultured on media inductive and non-inductive for embryogenesis and analyzed for differences in their chromosomal proteins and chromatin template activity. Non-histone proteins were prepared from dehistonized chromatin and their properties were investigated. Non-histone proteins proved to be acidic and associated easily with calf thymus histone. Non-histone proteins were able to counteract the inhibitory effect of histone on DNA-directed RNA synthesis in vitro. Almost the same rate of restoration occurred regardless of the interaction between DNA and protein, when sufficient amounts of non-histone proteins were added. However, once the histone-DNA complex was established, the restoration by non-histone proteins at comparably lower concentration was poor. Another acidic protein, bovine serum albumin, had no effect on histone inhibited RNA synthesis. Also non-histone proteins enhanced the chromatin directed RNA synthesis more than 100%. The template activity of chromatin changed after the inductive treatment of embryo formation and induced cells showed higher template activity than non-indiiced controls after embryo cells were formed. Histone components were the same in inductive and non-inductive cells. On the other hand, there was a correlation between template activity and the stimulation by non-histone proteins of histone-inhibited RNA synthesis.     

Nature of hydrocortisone-elicited amplification of template activity of liver chromatin.

The template efficiency of euchromatin region and number of RNA polymerase binding sites on this region of rat liver chromatin were significantly elevated at 3.5 h after administration of hydrocortisone to adrenalectomised rats. The euchromatin from the liver chromatin of horomone-treated rats was also found to have significantly increased levels of nonhistone proteins as compared to those in euchromatin fraction derived from adrenalectomised rats.     

Nature of RNA synthesis on embikhin-damaged templates

Embichin, a bifunctional alkylating mutagenic agent, inhibits RNA-synthesizing capacity of DNA and chromatin. The template capacity for decreasing the embichin-injured chromatin is caused by substantial reduction in the number of RNA molecules synthesized by this template. When DNA extracted from embichin-injured chromatin is used as a template, its template restriction is accounted for by an approximately 5-fold decrease in the RNA average molecular weight. The deoxyribonucleoprotein complexes reconstituted from embichin-injured DNA and control chromatic proteins had a lower template capacity compared with that of DNP reconstituted from control DNA. It is concluded that both links between DNA and proteins and DNA injuries are responsible for the inhibition of genome template capacity.     

Effect of RNA synthesis on the binding of 3H-cortisol to nuclear ribonucleoprotein particles from rat liver carrying DNA-like RNA in vivo.

3H-cortisol was found to associate with rat liver nuclear 30S ribonucleoprotein particles carrying D-RNA in vivo. No interaction was detectable when RNA synthesis was inhibited by alpha-amanitine. The association appears to be specifically for RNP carrying RNA synthesized after the administration of cortisol to adrenalectomized rats. The DNA/protein/RNA ratio of rat liver nuclei was not effected by alpha-amanitine under our conditions. However, the drug caused a 5-10 fold decrease in nuclear uptake of cortisol. The results are discussed in relation to a supposed transfer of cortisol-receptor complexes from the chromatin template to the nascent RNA chains.     

Preparation and characteristics of a wheat embryo cell-free extract active in the synthesis of high molecular weight viral polypeptides

Wheat embryo extracts are commonly used in cell-free protein synthesis studies. Soluble inhibitor(s) that diminish aminoacylation of tRNA exist in such extracts. These inhibitors can be effectively removed by prolonged dialysis, provided that proper salt conditions are maintained to ensure stability of the extract. The system, when only partially depleted of inhibitors, does not effectively support translation of certain classes of messengers, i.e., brome mosaic virus RNA 1 and RNA 2. All four proteins expected as the products of translation of BMV RNA, including peptides of molecular weight approaching 120,000, are formed in the fully active system. At limiting concentrations of template, the fully activated system incorporates the following amounts of [¹⁴C]leucine per microgram of template: Qβ RNA, 4.5 pmol; reovirus mRNA, 200 pmol, tobacco mosaic virus RNA, 227 pmol, and brome mosaic virus, up to 350 pmol.     

In vitro synthesis of RNA with “aggregate” enzyme,chromatin, and DNA from liver of methylazoxymethanol acetate-treated rats

“Aggregate” enzyme, chromatin and DNA preparations were isolated from livers of rats treated with the carcinogen, methylazoxymethanol (MAM) acetate. DNA template activity for RNA synthesis in vitro was unimpaired while the template activity of chromatin was slightly reduced. There was a marked inhibition of UTP incorporation into RNA, however, when the “aggregate” enzyme preparation was the source of both template and RNA polymerase. Circular dichroism analysis of the “aggregate” enzyme preparation indicated a change in conformation of the protein component. The results suggest that MAM acetate interacts with nuclear proteins and produces conformational changes which result in a decreased RNA synthesis.     

Transport of functional messenger RNA from liver nuclei in a reconstituted cell-free system

The reliability of a reconstituted cell-free system for messenger RNA processing and transport, consisting of isolated nuclei in fortified cytosol, has been evaluated in terms of the functionality and regulated release of the transported product. The poly(A) messenger RNA transport in vitro formed appropriate initiation complexes with ribosomes in an optimized translation system and had template activity comparable to that transported in vivo. The intra-nuclear origin of this messenger RNA is supported by pulse-labeling studies, its transport from detergent-treated nuclei and the absence of the release under non-transport conditions. Serum albumin was identified by immunoprecipitation and electrophoresis as one of the products synthesized when the transported RNA was translated in vitro. The transport of messenger RNA in the cell-free system was dependent on specific cytosol (soluble cytoplasmic) proteins. These proteins, which constitutes less than 0.1% of the total cytosol proteins, are precipitated wtih streptomycin with high specificity.