An amber suppressor tRNA gene derived by site-specific mutagenesis: cloning and function in mammalian cells

We describe the synthesis, cloning, expression, and in vivo function of a suppressor tRNA gene in mammalian cells. By using "primer-directed mutagenesis" on a Xenopus laevis tyrosine tRNA gene cloned into the recombinant single-strand phage M13mp5, we have generated an amber suppressor tRNA gene that has a nucleotide change--GTA leads to CTA--in the anticodon sequence. The suppressor (Su) tRNA gene was introduced into monkey kidney cells (CV-1) by using simian virus 40 (SV40) DNA as vector (SV40-tRNATyrSu+). CV-1 cells infected with virus containing the mutant, but not the wild-type, tRNA gene produce a functional amber suppressor tRNA as indicated by suppression of amber mutations in co-infecting adenovirus serotype 2-SV40 hybrids. Further evidence that suppression of these amber mutations is tRNA mediated was derived by isolation of total tRNA from CV-1 cells infected with the SV40-tRNATyr (Su+) recombinant and its use in demonstration of read through of an amber codon during in vitro translation of tobacco mosaic virus RNA in reticulocyte extracts. Interestingly, the amplification of an amber suppressor gene in CV-1 cells does not interfere with SV40 production, suggesting that suppression of amber codons may not be very deleterious to mammalian cell metabolism.

Expression of a X. laevis tRNATyr gene in mammalian cells

Expression of a X. laevis tRNATyr gene has been studied in mammalian cells. This tRNATyr gene has a 13 base intervening sequence adjacent to its anticodon. A fragment containing the tRNATyr gene was cloned into the late region of SV40. Cells infected with a recombinant virus stock vastly overproduce a tRNATyr that is properly spliced, processed and modified. It was also found that the X. laevis tRNATyr is identical or nearly identical to an endogenous tRNATyr of monkey kidney cells. The possibility of using the X. laevis tRNATyr gene to create an amber suppressor for mammalian cells is discussed.

T antigen repression of SV40 early transcription from two promoters

The SV40 early mRNAs encode large (T) and small (t) tumor antigens. During the lytic cycle, the 5' termini of the early mRNAs undergo a shift: shortly after infection only an initiation site downstream from the TATA box is utilized; later an upstream initiation site becomes prominent. Both initiation sites are utilized in an in vitro transcription extract. D2T, a T antigen analog, specifically represses transcription in vitro from both initiation sites, but at different concentrations. Binding of D2T to site I suppresses initiation from the site downstream of the TATA box; binding to sites II and I suppresses initiation from the upstream site. The role of T antigen binding in repression of transcription and in the shift of initiation sites on the early strand is discussed.

Inhibition of transcription factor activity by poliovirus

To study the poliovirus-induced inhibition of host-cell RNA synthesis, we prepared transcription extracts from mock-infected and poliovirus-infected HeLa cells. In contrast with the control extracts, poliovirus-infected cell extracts prepared 3 hr after infection were unable to transcribe specifically DNA templates recognized by RNA polymerase II. Accurate transcription by RNA polymerase III, however, was only slightly reduced. Supplementation of the infected cell extract with a crude preparation of transcription factors (S100) restored its ability to transcribe a polymerase II template specifically; supplementation with purified polymerase II had no effect. When the S100 was fractionated on a phosphocellulose column, the restoration activity eluted between 0.35 M and 1 M KCl. When we tested infected extracts for inhibitory activity by mixing uninfected and infected cell extracts, no in vitro inhibition of polymerase II transcription by the uninfected extract was evident. These results indicate that at least one factor required for specific transcription by polymerase II is deficient in extracts from poliovirus-infected cells.

In vitro transcription of adenovirus

A series of recombinants of adenovirus DNA fragments and pBR322 was used to test the transcriptional activity of the nine known adenovirus promoters in a cell-free extract. Specific initiation was seen at all five early promoters as well as at the major late promotor and at the intermediate promoter for polypeptide IX. The system failed to recognize the two other adenovirus promoters, which were prominent in vivo only at intermediate and late stages in infection. Microheterogeneity of 5' termini at several adenovirus promoters, previously shown in vivo, was reproduced in the in vitro reaction and indeed appeared to result from heterogeneous initiation rather than 5' processing. To test for the presence of soluble factors involved in regulation of nRNA synthesis, the activity of extracts prepared from early and late stages of infection was compared on an assortment of viral promoter sites. Although mock and early extracts showed identical transcription patterns, extracts prepared from late stages gave 5- to 10-fold relative enhancement of the late and polypeptide IX promoters as compared with early promoters.

Sequential transcription-translation of simian virus 40 by using mammalian cell extracts

Ribonucleic acids (RNAs) transcribed in vitro by using the whole-cell extract system of Manley et al. (Proc. Natl. Acad. Sci. U.S.A. 77:3855-3859, 1980) were tested for their efficiency and fidelity in directing protein synthesis in reticulocyte lysates. Simian virus 40 deoxyribonucleic acid (DNA), cleaved by various restriction endonucleases, was used as the template. Successful translation of the small tumor antigen t, as well as the capsid proteins VP1, VP2, and VP3, was detected by immunoprecipitation analysis. Although no synthesis of large T antigen was detected, use of this technology allows detection of large T synthesis resulting from the correct splicing of as little as 0.2% of the in vitro RNA transcripts, making it ideal for use as an in vitro splicing assay. Transcripts synthesized in vitro were used as messages at least as efficiently as were viral messenger RNA's (mRNA's) synthesized in vivo; and in the case of small t, there was more efficient translation of small t mRNA synthesized in vitro than of small t mRNA synthesized in vivo. The transcripts that served as mRNA's for the various polypeptides were identified by using the following two criteria. (i) The sensitivity of synthesis of a given protein to digestion of the template DNA with restriction enzymes allowed the localization of the promoter and coding regions. (ii) Translation of size-fractionated RNA allowed confirmation of the transcript-mRNA assignments. With these techniques we found that VP2, VP3 and, in some cases, VP1 synthesis resulted from the initiation of translation at internal AUG codons. In fact, families of polypeptides were produced by initiation of translation at AUG codons within sequences coding for VP1 and T, presumably as a result of transcription initiation events that generated 5' ends immediately upstream from these AUGs. Application of this technology for the identification of coding regions within cloned DNA fragments is discussed.

Expression of early adenovirus genes requires a viral encoded acidic polypeptide

Host-range mutants of adenovirus 5 that contain a defect in region E1A (0-4.5 units) fail to replicate in HeLa cells and to transform rodent cells. In HeLa cells, these mutants synthesize only the two RNAs from E1A that share the same 5' and 3' termini but differ in length by the amount of internal sequence removed by splicing. RNA from wild-type virus, selected by hybridization to DNA from region E1A, translates into polypeptides of Mr 51,000 and 48,000 that are highly acidic in isoelectric focusing gels. These acidic Mr 51,000 and Mr 48,000 polypeptides are encoded by the longer and shorter E1A RNAs, respectively. Two of the host-range mutants, H5hr1 and H5hr2, fail to synthesize the Mr 51,000 polypeptide but do produce the Mr 48,000 polypeptide and a novel polypeptide thought to be a truncated portion of the Mr 51,000 polypeptide. H5hr1 and H5hr2 are hypothesized to have termination codons in sequences found only in RNA encoding the Mr 51,000 polypeptide. This prediction is verified for H5hr1 by DNA sequence analysis. The other three host-range mutants (H5hr3-5) synthesize both acidic polypeptides and are predicted to be missense. These results strongly imply that the Mr 51,000 polypeptide, alone or in combination with the Mr 48,000 polypeptide, is needed to regulate expression of adjacent viral genes during the early phase of adenovirus infection.

SV40 DNA transfection of cells in suspension: analysis of efficiency of transcription and translation of T-antigen

A modification of the Graham and Van der Eb (1974) DNA-calcium phosphate coprecipitation technique is shown to routinely transfect 15% of CV-1 cells with SV40 DNA. The transfection is done in suspension after detachment of cells by trypsin digestion. Transfection efficiency was measured by staining cells for the presence of SV40 T-antigen by indirect immunofluorescence and by assaying for the presence of SV40 early message by the Berk and Sharp (1978) technique.

A gene chimaera of SV40 and mouse beta-globin is transcribed and properly spliced

A gene chimaera of the first exon from simian virus 40 (SV40) sequences coding for T antigen placed upstream from the third exon from mouse beta-globin, and separated by the resultant new chimaeric intron, was cloned into a bacterial plasmid. When transfected into monkey cells, the gene chimaera was transcribed, polyadenylated and spliced using the donor splice site from SV40 and the acceptor splice site from mouse beta-globin. This result suggests that a donor site from one gene can be spliced to an acceptor site from another gene.

Transcription of Simian virus 40 DNA in a HeLa whole cell extract

Extracts of HeLa cells containing RNA polymerase II and other factors recognize specific sites on linear simian virus 40 (SV40) DNA for initiation of transcription. The most prominent RNA products transcribed from the early region of SV40 and th E strand are initiated at sites 0.67 and 0.655 on the SV40 map. These two RNAs are synthesized by polymerase II. Their 5' termini were positioned by sizing transcripts that extend from the initiation site to the end of the template restriction endonuclease fragment, and by S1-nuclease mapping of unlabeled RNA using DNA probes labeled at their 5' termini. The limit of resolution of mapping of 5' termini is approximately 25 nucleotides. RNAs with 5' termini at similar positions have been found during characterization of mRNAs produced in infected cells. Thus, the whole cell extract is probably initiating transcription on linear SV40 DNA in vitro at the same sites as RNAs synthesized in vivo. Two other processes frequently involved in mammalian cell mRNA biosynthesis, creation of specific 3'-terminal polyadenine tracts and RNA splicing, were not detected during the course of these studies.

Regulation of adenovirus mRNA synthesis

The lytic cycle of adenovirus is a tightly regulated sequence of stages. When this regulation is studied at the level of mRNA production, the most significant step in controlling gene expression is initiation of transcription. Thus in preceding from one stage of expression to another, viral factors seem to turn on transcription of new sets of genes. At the moment, it is thought that viral mRNA synthesis involves initiation of transcription at ten different promoter sites. It is likely that in some manner the frequency of an initiation of transcription at nine of these sites is affected by one or more viral gene products. With the recent development of soluble in vitro transcription systems that respond to exogenously added DNA, it should be possible to begin to study regulation of gene expression at this stage of transcription. At present, these systems yield the paradoxical observation that extracts prepared from uninfected human cells more efficiently recognize the late promoter as compared to the early promoter of adenovirus. As more is learned about regulation of synthesis of viral mRNAs, examples will surely be found where RNA processing and RNA turnover play a critical role in determining the level of mRNAs. Such cases are more likely to appear in the balancing of synthesis of different mRNAs derived from one transcriptional unit. Few experiments have been directed to this possibility and the study of adenovirus molecular biology is only now entering the age of maturity where these experiments are feasible.

DNA-dependent transcription of adenovirus genes in a soluble whole-cell extract

We have developed a cell-free system for studying the synthesis of mRNA in mammalian cells. The system consists of a dialyzed and concentrated whole-cell extract derived from HeLa cells, small molecules and cofactors needed for transcription, and exogenously added DNA. Accurate transcription by RNA polymerase II is entirely dependent upon addition of promoter-containing eukaryotic DNA. At optimal DNA and extract concentrations, transcription initiation from the adenovirus serotype 2 late promoter is readily detectable, and specific transcripts over 4000 nucleotides in length are observed. The RNA synthesized in vitro contains the same 5' capped RNase T1 undecanucleotide as does the in vivo transcript. RNA synthesis also initiates accurately at both an early and an intermediate adenovirus promoter site.

Expression of early and late simian virus 40 transcripts in the absence of protein synthesis

We examined the synthesis of early and late simian virus 40 (SV40) mRNA's in SV40-infected cells treated with two kinds of protein synthesis inhibitors. SV40 stimulated the synthesis of mRNA's for both large and small tumor antigens in cells pretreated with the drug emetine before the addition of virus. Emetine is a stringent inhibitor of protein synthesis and, thus, protein factors necessary for transcription and processing of these mRNA's probably preexist in the cell. Surprisingly, infection of cells pretreated with the protein synthesis inhibitor cycloheximide stimulated the synthesis of about 10-fold-higher levels of early viral mRNA's than did comparable infections of nontreated cells. This amplification of early viral mRNA steady-state levels is probably not due to inhibition of synthesis of the early A gene product since the same degree of drug-specific amplification was seen in SV40 tsA-infected cells that were cultured at the nonpermissive temperature. However, the most interesting effect of cycloheximide addition on viral mRNA synthesis was its stimulation of the appearance of late mRNA's in the cytoplasm of cells at early periods of infection. The synthesis of late mRNA's does not appear to require the A gene product as late RNAs can be found in the cytoplasm of cells infected with SV40 tsA mutants which have been maintained at 41 degrees C and continuously cultured in the presence of cycloheximide.

Comparative study of different isolates of murine sarcoma virus

The RNA genomes of a variety of murine sarcoma viruses (MSV) were compared by heteroduplex analysis. These viruses included the Moloney-derived isolates 124-MSV, m1-MSV, m3-MSV, HT1-MSV, and NP-MSV and also two independent isolates, Gazdar MSV and 1712-MSV. All of these viral genomes exhibited the acquired cellular sequences previously identified in 3124-MSV and thought to be responsible for transformation and sarcomagenesis. The location of the acquired cellular sequences within the envelope gene was variable in different MSV isolates, suggesting that the cellular sequences can be expressed in different positions relative to murine leukemia virus-derived information present in MSV. Deletions in the gag coding region of the different MSVs were consistent with their known gag-related gene products. Based on several features of the hetero-duplex analysis and the known genealogical relationships of the different MSVs, various possible mechanisms for the formation of MSV are considered.

Cloning and nucleotide sequence of DNA coding for bovine preproparathyroid hormone

We have cloned in Escherichia coli a DNA copy of mRNA coding for bovine preproparathyroid hormone. Double-stranded DNA was inserted into the Pst I site in plasmid pBR322 by using the poly(dG)-poly(dC) homopolymer extension technique to join the DNA molecules. Recombinant plasmids coding for preproparathyroid hormone were identified by the plasmid's ability to arrest specifically the translation of preproparathyroid hormone mRNA. The nucleotide sequence of the largest recombinant was determined by using both chemical and enzymatic techniques. The parathyroid insert contains 470 nucleotides--102 nucleotides from the 5' noncoding region of the mRNA, 345 nucleotides representing the entire coding region, and 23 nucleotides from the 3' noncoding region. The coding sequence clarifies the hormone's amino acid sequence, which has been disputed. Codon usage is discussed.