Transcriptions of the bacteriophage T4 template in vitro: separation of "delayed early" from "immediate early" transcription

Selective transcription in response to an inflammatory stimulus

An inflammatory response is initiated by the temporally controlled activation of genes encoding a broad range of regulatory and effector proteins. A central goal is to devise strategies for the selective modulation of proinflammatory gene transcription, to allow the suppression of genes responsible for inflammation-associated pathologies while maintaining a robust host response to microbial infection. Toward this goal, recent studies have revealed an unexpected level of diversity in the mechanisms by which chromatin structure and individual transcription factors contribute to the selective regulation of inflammatory genes.

Without a license, or accidents waiting to happen

This is a memoir of circumstances that have shaped my life as a scientist, some of the questions that have excited my interest, and some of the people with whom I have shared that pursuit. I was introduced to transcription soon after the discovery of RNA polymerase and have been fascinated by questions relating to gene regulation since that time. My account touches on early experiments dealing with the ability of RNA polymerase to selectively transcribe its DNA template. Temporal programs of transcription that control the multiplication cycles of viruses (phages) and the precise mechanisms generating this regulation have been a continuing source of fascination and new challenges. A longtime interest in eukaryotic RNA polymerase III has centered on yeast and on the enumeration and properties of its transcription initiation factors, the architecture of its promoter complexes, and the mechanism of transcriptional initiation. These areas of research are widely regarded as separate, but to my thinking they have posed similar questions, and I have been unwilling or unable to abandon either one for the other. An additional interest in archaeal transcription can be seen as stemming naturally from this point of view.

De novo protein synthesis is required for lytic cycle reactivation of Epstein-Barr virus, but not Kaposi's sarcoma-associated herpesvirus, in response to histone deacetylase inhibitors and protein kinase C agonists

The oncogenic human gammaherpesviruses, Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV), are latent in cultured lymphoma cells. We asked whether reactivation from latency of either virus requires de novo protein synthesis. Using Northern blotting and quantitative reverse transcriptase PCR, we measured the kinetics of expression of the lytic cycle activator genes and determined whether abundance of mRNAs encoding these genes from either virus was reduced by treatment with cycloheximide (CHX), an inhibitor of protein synthesis. CHX blocked expression of mRNAs of EBV BZLF1 and BRLF1, the two EBV lytic cycle activator genes, when HH514-16 Burkitt lymphoma cells were treated with histone deacetylase (HDAC) inhibitors, sodium butyrate or trichostatin A, or a DNA methyltransferase inhibitor, 5-Aza-2'-deoxycytidine. CHX also inhibited EBV lytic cycle activation in B95-8 marmoset lymphoblastoid cells by phorbol ester phorbol-12-myristate-13-acetate (TPA). EBV lytic cycle induction became resistant to CHX between 4 and 6 h after application of the inducing stimulus. KSHV lytic cycle activation, as assessed by ORF50 mRNA expression, was rapidly induced by the HDAC inhibitors, sodium butyrate and trichostatin A, in HH-B2 primary effusion lymphoma cells. In HH-B2 cells, CHX did not inhibit, but enhanced, expression of the KSHV lytic cycle activator gene, ORF50. In BC-1, a primary effusion lymphoma cell line that is dually infected with EBV and KSHV, CHX blocked EBV BRLF1 lytic gene expression induced by TPA and sodium butyrate; KSHV ORF50 mRNA induced simultaneously in the same cells by the same inducing stimuli was resistant to CHX. The experiments show, for the cell lines and inducing agents studied, that the EBV BZLF1 and BRLF1 genes do not behave with "immediate-early" kinetics upon reactivation from latency. KSHV ORF50 is a true "immediate-early" gene. Our results indicate that the mechanism by which HDAC inhibitors and TPA induce lytic cycle gene expression of the two viruses differs and suggest that EBV but not KSHV requires one or more proteins to be newly synthesized between 4 and 6 h after application of an inducing stimulus.

A physical map of bacteriophage T4 including the positions of strong promoters and terminators recognized in vitro

We present a linearized physical map of the genome of bacteriophage T4. This map contains the cleavage sites for restriction enzymes SmaI, KpnI, SalI, BglII, XhoI, XbaI, ClaI , HaeII, EcoRI, and EcoRV . It also contains about 200 TaqI sites. The promoter sites recognized in vitro and a number of rho independent terminators have also been mapped.

In vitro system for induction of delayed early RNA of bacteriophage T4

Concentrated lysates of Escherichia coli that had been infected with bacteriophage T4 in the presence of chloramphenicol show the same restriction of transcription in vitro as is found in vivo. Restricted lysates can be complemented with lysates from infected cells to induce production of delayed early RNA. Complementation takes place between the RNA polymerase of the restricted lysate and the DNA of the unrestricted lysate. We present evidence that delayed early RNA in these lysates is initiated at quasi-late (middle) promoters, and that such recognition is related to changes in the state of the template DNA.

Synthesis of functional bacteriophage T4-delayed early mRNA in the absence of protein synthesis

When Escherichia coli B207 is grown either aerobically or under limited aerobic conditions, pretreated with chloramphenicol to block protein synthesis, and then infected with bacteriophage T4, the phage RNA which accumulates, termed "immediately early" (IE), contains the transcripts of a limited number of prereplicative genes. Among the transcripts which accumulate is the mRNA which serves as a template for deoxycytidylate hydroxymethylase (HMase) synthesis. Among the prereplicative gene transcripts which do not accumulate under these conditions are deoxycytidine triphosphatase (dCTPase), alpha-glucosyl transferase (alphg-gt), and deoxynucleotide kinase (kinase); these genes have been termed "delayed early" (DE). In contrast, when protein synthesis is inhibited by depleting aerobically grown E. coli B207 of K+, both IE and DE T4 RNA accumulate, but these transcripts do not contain functional HMase, dCTPase, alpha-gt, or kinase mRNA's. However, if E. coli is grown under conditions of limited aeration and then depleted of K+ prior to T4 infection, the T4 RNA which accumulates contains both IE and DE transcripts and functional HMase, dCTPase, and alpha-gt mRNA's. Functional kinase mRNA does not accumulate under these conditions. The results of these experiments indicate that the synthesis of functional DE RNA in the absence of simultaneous protein synthesis, depends on the physiological condition of the cells and the way in which protein synthesis is inhibited. In addition, data is presented which suggests that extensive transcription of DE genes in the absence of protein synthesis results in the inhibition of transcription of certain IE genes.

Transcriptional regulation of T4 bacteriophage-specific enzymes synthesized in vitro

In contrast to dihydrofolate reductase and four other phage-specific enzymes, the initiation of deoxynucleotide kinase is essentially prevented if rifampin is added to a culture of Escherichia coli B cells within 1.5 min after infection with T4. Deoxynucleotide kinase thus belongs to a group of so-called delayed-early enzymes that is not initiated from an immediate-early promoter site. We prepared crude extracts from infected cells in a manner designed to maintain the integrity of the complexes of native, endogenous T4 DNA with bacterial structural and enzymatic units concerned with RNA synthesis. The initiation of the synthesis of the mRNA for dihydrofolate reductase, an example of an immediate-early enzyme, and deoxynucleotide kinase, a special type of delayed-early enzyme, was studied with these extracts prepared from cells infected in the absence or presence of chloramphenicol. Initiation of transcription of the dihydrofolate reductase gene is immediate when programmed by extracts made either from cells treated with chloramphenicol prior to infection (CM extracts) or from cells 3 min into the normal infection cycle (3-min extracts). However, initiation of transcription of the deoxynucleotide kinase gene programmed by CM extracts is delayed 2 min relative to the immediate initiation of transcription of the deoxynucleotide kinase gene programmed by 3-min extracts. These experiments duplicated in vitro effects of the antibiotics on the synthesis of phage-specific mRNA previously noted only in vivo.

Initiation characteristics for the synthesis of five T4 phage-specific messenger RNAs in vitro

The involvement of the nucleoside triphosphates in the initiation of the synthesis of the messenger ribonucleic acid of five T4 specific enzymes has been studied. Only one of these, the messenger RNA for deoxynucleosidemonophosphate kinase, can be initiated in the presence of one nucleoside triphosphate, namely ATP. All of the remaining four require the presence of at least two nucleoside triphosphates during the initiation period. The combination of ATP and UTP was best for the initiation of messenger RNA for dihydrofolate reductase, ATP and CTP for deoxycytidylate hydroxymethyltransferase and beta-glucosyltransferase, and ATP and GTP for alpha-glucosyltransferase. We have concluded that there is a great variation in the nucleotide composition and sequence of the initiation sites in T4 DNA. No correlation in the requirements of nucleoside triphosphates during the initiation period could be observed among the five systems studied according to their classification as one type or another of "early" T4 messenger RNA.

Cold-sensitive Pseudomonas RNA polymerase. II. Cold-promoted restriction of bacteriophage CB3 and the lack of host-dependent bacteriophage-specific RNA transcription

Cold-sensitive restriction of Pseudomonas phage CB3 by Pseudomonas aeruginosa strain PAT2 involves some aspect of CB3 specific RNA synthesis at 20 C. Experiments using chloramphenicol treatment and RNA-DNA hybridization establish that the amount of CB3 RNA present at 20 C is consistent with the known percentage of phage yielder cells at 20 C. Thus, it appears that nonyielder cells of PAT2 synthesize little or no phage-specific mRNA. Burgess technique extracted PAT2 RNA polymerase (RNAP) is cold sensitive when assayed in vitro with CB3 DNA at 20 C. However, it is not cold sensitive when either calf thymus or PAT2 DNA are the templates for transcription. Low ionic strength assay conditions eliminate the cold sensitivity of PAT2 RNAP. The effect of low ionic environments on transcription initiation along with the in vivo and in vitro suppression of cold sensitivity by host rifampin resistance suggests that the inability of CB3 to reproduce in PAT2 at 20 C is a cold-sensitive step in host RNAP initiation. Our modified RNAP extraction procedure for PAT2 and PAO1C also results in the recovery of cold-sensitive PAT2 RNAP with respect to CB3 DNA templates and points to basic enzymological differences between the two hosts. A model is presented for the unusual influence of temperature on the initiation process of both PAT2 and PAO1C on RNAP transcription.

Transcription units in bacteriophage T4

We have investigated the possibility of assigning genes of T4 bacteriophage to their units of transcription (scriptons) by studying gene expression from UV-irradiated DNA templates. Since RNA chains are prematurely terminated on UV-irradiated DNA templates and since the promotor distal part of the RNA chain is deleted, the expression of any gene is inversely proportional to the distance between the promotor and the promotor distal end of the gene. We find that the early genes, 43, 45 and rIIB, are promotor proximal. Since at least genes 43 and rIIB are classified as delayed early genes, these results suggest that their synthesis may require the recognition of new promotors. Additional early genes (44, 62, 42, 46, 47, 55, and rIIA) and some late genes (34, 37, and 38) have also been assigned positions relative to their promotors.

Gene expression during the development of Bacillus subtilis bacteriophage phi 29. I. Analysis of viral-specific transcription by deoxyribonucleic acid-ribonucleic acid competition hybridization

The ribonucleic acid (RNA) specified by bacteriophage phi29 was analyzed to determine its composition at various times in the viral lytic cycle. Although viral-specific RNA was detected immediately after infection, a large increase in the rate was observed at 10 min when DNA synthesis began. phi29 was found to resemble other viruses in that gene expression occurred in two stages which could be defined temporally as "early" and "late." Early RNA appeared before the onset of viral deoxyribonucleic acid (DNA) replication and accounted for approximately 40% of the viral genetic potential. This RNA was also present late in the infectious cycle because of the slow turnover rate of phi29-specific RNA (approximately 10 min half-life) and the continued synthesis of much early viral RNA throughout infection. Late RNA was first detected at approximately the same time as viral DNA replication, although late transcription was not dependent upon DNA synthesis. This RNA was only partially displaced by early RNA in the appropriate competition experiments, suggesting that it contained sequences not present in the early class. Expression of viral genes was sensitive to rifamycin throughout the lytic cycle, the sensitivity resulting from a dependence upon the rifamycin phenotype of the host RNA polymerase.

Gene expression during the development of Bacillus subtilis bacteriophage phi29. II. Resolution of viral-specific ribonucleic acid molecules

The ribonucleic acid (RNA) specified by bacteriophage phi29 was isolated under conditions which minimized physical and enzymatic degradation, reduced aggregation, and enriched for completed molecules. This RNA was fractionated both by sedimentation through sucrose density gradients and electrophoresis through polyacrylamide gels to measure the size and relative amount of each component. Early RNA consisted of six components of molecular weight 0.75 x 10(6), 0.44 x 10(6), 0.37 x 10(6), 0.25 x 10(6), 0.09 x 10(6), and 0.04 x 10(6), accounting for 35% of the coding capacity of phi29 deoxyribonucleic acid (DNA). All of these components except the one at 0.44 x 10(6) were detected when infection occurred in the presence of chloramphenicol. Synthesis of the major early component (0.75 x 10(6)) ceased shortly after the onset of viral DNA synthesis. The other species of early RNA were synthesized throughout the latent period. Three additional components, 1.75 x 10(6), 0.93 x 10(6), and 0.07 x 10(6), appear at late times. The two large RNAs may be polycistronic messenger RNAs corresponding to the seven viral capsid proteins.

DNA-directed synthesis in vitro of T4 phage-specific enzymes

The synthesis of deoxynucleotide kinase (EC 2.7.4.2) in vitro by a preparation consisting of T4 bacteriophage DNA and a cell-free extract of Escherichia coli has been reported. A study of the role of monovalent cations in the synthesis of this enzyme as well as alpha-glucosyl transferase (EC 2.4.1.2) shows that potassium ions are required for maximal enzyme production. Examination of the RNA-directed system indicates that potassium ions are more effective than ammonium ion in the translation of messenger RNA for the formation of the biologically active proteins studied. From a comparison of the magnitude of the effect of ions on both the DNA- and RNA-directed systems, we conclude that potassium ions may also have a marked stimulatory effect on transcription of the deoxynucleotide kinase gene of T4 DNA. The time required for messenger initiation and completion and the size distribution of messenger RNA formed in vitro were also examined.

The temporal expression of T2r + bacteriophage genes in vivo and in vitro

The kinetic order of synthesis of deoxycytidylate deaminase (EC 3.5.4.12), deoxycytidylate hydroxymethylase (EC 2.1.2.b), dihydrofolate reductase (EC 1.5.1.3), 5-hydroxymethyldeoxycytidylate kinase (EC 2.7.4.4), and thymidylate synthetase (EC 2.1.1.b) after infection of Escherichia coli with T2r(+) bacteriophage was found not to correlate with their order of synthesis in an in vitro protein-synthesizing preparation. The in vivo and in vitro synthesis of enzyme-specific messenger RNA measured in the protein-synthesizing preparation preceded each enzyme by about 1 min. Through the use of sheared DNA, it was shown that the thymidylate synthetase gene was most susceptible to a loss in template activity, which suggests that this gene is further removed from its promoter than the other genes are from theirs. With a DNA segment of 2.5 x 10(5) daltons, the synthesis of dihydrofolate reductase alone was obtained, but at a much reduced rate. Translation of the RNA from phage-infected cells treated with chloramphenicol yielded amounts of dihydrofolate reductase and deoxycytidylate hydroxymethylase activities similar to those obtained with RNA from untreated infected cells. These results suggest that the chloramphenicol RNA, which consists primarily of immediate-early RNA, may contain most, if not all, of the information required for the synthesis of phage dihydrofolate reductase and deoxycytidylate hydroxymethylase.