Double-stranded RNA binding by human cytomegalovirus pTRS1

The human cytomegalovirus (HCMV) TRS1 and IRS1 genes rescue replication of vaccinia virus (VV) that has a deletion of the double-stranded RNA binding protein gene E3L (VVDeltaE3L). Like E3L, these HCMV genes block the activation of key interferon-induced, double-stranded RNA (dsRNA)-activated antiviral pathways. We investigated the hypothesis that the products of these HCMV genes act by binding to dsRNA. pTRS1 expressed by cell-free translation or by infection of mammalian cells with HCMV or recombinant VV bound to dsRNA. Competition experiments revealed that pTRS1 preferentially bound to dsRNA compared to double-stranded DNA or single-stranded RNA. 5'- and 3'-end deletion analyses mapped the TRS1 dsRNA-binding domain to amino acids 74 through 248, a region of identity to pIRS1 that contains no homology to known dsRNA-binding proteins. Deletion of the majority of this region (Delta86-246) completely abrogated dsRNA binding. To determine the role of the dsRNA-binding domain in the rescue of VVDeltaE3L replication, wild-type or deletion mutants of TRS1 were transfected into HeLa cells, which were then infected with VVDeltaE3L. While full-length TRS1 rescued VVDeltaE3L replication, deletion mutants affecting a carboxy-terminal region of TRS1 that is not required for dsRNA binding failed to rescue VVDeltaE3L. Analyses of stable cell lines revealed that the carboxy-terminal domain is necessary to prevent the shutoff of protein synthesis and the phosphorylation of eIF2alpha after VVDeltaE3L infection. Thus, pTRS1 contains an unconventional dsRNA-binding domain at its amino terminus, but a second function involving the carboxy terminus is also required for countering host cell antiviral responses.     

Sequence and translation of the murine coronavirus 5''-end genomic RNA reveals the N-terminal structure of the putative RNA polymerase.

A 28-kilodalton protein has been suggested to be the amino-terminal protein cleavage product of the putative coronavirus RNA polymerase (gene A) (M.R. Denison and S. Perlman, Virology 157:565-568, 1987). To elucidate the structure and mechanism of synthesis of this protein, the nucleotide sequence of the 5' 2.0 kilobases of the coronavirus mouse hepatitis virus strain JHM genome was determined. This sequence contains a single, long open reading frame and predicts a highly basic amino-terminal region. Cell-free translation of RNAs transcribed in vitro from DNAs containing gene A sequences in pT7 vectors yielded proteins initiated from the 5'-most optimal initiation codon at position 215 from the 5' end of the genome. The sequence preceding this initiation codon predicts the presence of a stable hairpin loop structure. The presence of an RNA secondary structure at the 5' end of the RNA genome is supported by the observation that gene A sequences were more efficiently translated in vitro when upstream noncoding sequences were removed. By comparing the translation products of virion genomic RNA and in vitro transcribed RNAs, we established that our clones encompassing the 5'-end mouse hepatitis virus genomic RNA encode the 28-kilodalton N-terminal cleavage product of the gene A protein. Possible cleavage sites for this protein are proposed.     

In vitro translation of epidermal RNA from different anatomical regions and metamorphic stages of Hyalophora cecropia

Epidermal RNA isolated from different anatomical regions and metamorphic stages of Hyalophora cecropia was translated in vitro with commercial wheat germ and rabbit reticulocyte systems. The translation products were analyzed by 2D gel electrophoresis. The two systems yielded identical products if canine microsomal membranes were added to remove signal peptides from the reticulocyte products. The endogenous processing by the wheat germ extract occurred even in the presence of protease inhibitors. Some of the processed translation products co-migrated with unlabeled cuticular protein standards. All of the major cuticular proteins could be identified, but only when translations were carried out with RNA from epidermis underlying cuticle containing these proteins. Hence, cuticular protein distribution is due to differential synthesis and not to differential extractability. For larval abdominal RNA, most of the major translation products did not co-migrate with known larval cuticular proteins or with proteins synthesized and retained by the epidermis. These unknown products were lower in apparent molecular weight than the cuticular proteins. Their identity remains unknown; they may be premature translation products, but altering translation conditions did not reduce their abundance.     

Internal ribosome entry site within hepatitis C virus RNA.

The mechanism of initiation of translation on hepatitis C virus (HCV) RNA was investigated in vitro. HCV RNA was transcribed from the cDNA that corresponded to nucleotide positions 9 to 1772 of the genome by using phage T7 RNA polymerase. Both capped and uncapped RNAs thus transcribed were active as mRNAs in a cell-free protein synthesis system with lysates prepared from HeLa S3 cells or rabbit reticulocytes, and the translation products were detected by anti-gp35 antibodies. The data indicate that protein synthesis starts at the fourth AUG, which was the initiator AUG at position 333 of the HCV RNA used in this study. Efficiency of translation of the capped methylated RNA appeared to be similar to that of the capped unmethylated RNA. However, a capped methylated RNA showed a much higher activity as mRNA than did the capped unmethylated RNA in rabbit reticulocyte lysates when the RNA lacked a nucleotide sequence upstream of position 267. The results strongly suggest that HCV RNA carries an internal ribosome entry site (IRES). Artificial mono- and dicistronic mRNAs were prepared and used to identify the region that carried the IRES. The results indicate that the sequence between nucleotide positions 101 and 332 in the 5' untranslated region of HCV RNA plays an important role in efficient translation. Our data suggest that the IRES resides in this region of the RNA. Furthermore, an IRES in the group II HCV RNA was found to be more efficient than that in the group I HCV RNA.     

In vitro translation of RNA from lizard epididymis and identification of poly A RNA coding for a major androgen-dependent protein

During the reproductive period (spring) the lizard epididymis secretes a soluble protein of an apparent molecular weight (MW) of 19,000, the protein L. This androgen dependent protein disappears during post-nuptial atrophy of the epididymis (summer). At two time intervals (spring and summer) total RNA were extracted and poly (A) RNA were prepared. The RNA were translated in a cell-free system (rabbit reticulocyte lysate) in the presence of 35S methionine. Labelled translation products were analyzed by polyacrylamide gel electrophoresis under denaturing conditions. Electrophoresis were preceded or not by immunoprecipitation with an antiserum raised against protein L. RNA extracted during spring coded for several unique bands including five immunoprecipitated proteins with close-related MW (21,000 to 25,000). When RNA were translated in the presence of dog microsomes, the five previously detected protein bands disappear although a 19,000 MW immunoprecipitated protein was clearly demonstrated. These proteins were not detected when RNA extracted in summer were used. The protein L appears to be synthesized as preprotein(s). Its (unique or several?) messenger is of poly A type; it is present in spring and absent or undetectable in these experimental conditions in summer.     

Chromoplast-Targeted Proteins in Tomato (Lycopersicon esculentum Mill.) Fruit

The chloroplast to chromoplast transition during tomato (Lycopersicon esculentum Mill.) fruit ripening is characterized by a dramatic change in plastid structure and function. We have asked whether this process is mediated by an increase in the steady-state level of RNA for plastid targeted proteins. Assays for import of radiolabeled translation products into isolated pea (Pisum sativum L.) chloroplasts were used to monitor levels of chromoplast-targeted proteins at four stages of tomato fruit development. We have found striking increases during development in levels of translatable RNA for two such proteins. Additionally, the import of in vitro translation products was examined for seven individual cDNA clones known to encode RNA that increase during fruit ripening. Three of these clones produced in vitro translation products that were imported into pea chloroplasts. This implies that there is synthesis and import of new proteins during the transition from chloroplast to chromoplast and that the plastid conversion is an active developmental program rather than a simple decline in synthesis of the photosynthetic apparatus. Furthermore, our results demonstrate the utility of this method for identification of structural genes involved in plastid morphogenesis.     

Characterization of two SV40 early mRNAs and evidence for a nuclear "prespliced" RNA species.

Using in vitro translation of sucrose-gradient fractionated cytoplasmic mRNA from SV40-infected cells, we have shown that a deletion in the region mapping between 0.54--0.59 reduced the size of mRNA for small-t but not the size of mRNA for large-T. Mutants with a deletion in this region were shown to produce in vivo either shortened small-t or no small-t, and normal large-T. Similarly, in vitro translation of poly(A)+cytoplasmic RNA from cells infected with these mutants gave the same results. On the other hand in vitro translation of poly(A)+nuclear RNA from the mutants which made no small-t produced a small-t derivative possibly synthesized from a prespliced RNA species. We have also shown that poly(A)+nuclear RNA from mutant dl 2122 produced two small-t related proteins: one of these (MW: 11K) probably represents the product of a "prespliced" RNA, the other (MW: 17K) which is also found in the cytoplasm represents the product of the mutant specific small-t mRNA.     

Characterization of the major mRNAs transcribed from the genes for glycoprotein B and DNA-binding protein ICP8 of herpes simplex virus type 1.

The structural genes encoding the herpes simplex virus type 1 glycoprotein B and the major DNA-binding protein ICP8 have been mapped previously within the EcoRI-F restriction fragment (map coordinates 0.314 to 0.420) of the viral genome. In this study the mRNAs transcribed from these DNA sequences were identified by hybridization selection of 32P-labeled RNA and by Northern blot analysis of polyadenylated cytoplasmic RNA. A 3.4-kilobase RNA was the major mRNA homologous to the DNA sequences between coordinates 0.343 and 0.386 in which mutations in the glycoprotein B gene have been mapped. A 4.5-kilobase RNA was the major mRNA homologous to the viral DNA sequences between coordinates 0.361 and 0.417 in which mutations in the ICP8 gene have been mapped. Hybridization-selected mRNAs were translated in vitro to determine the primary translation products encoded in each region. The glycoprotein B- and ICP8-specific polypeptides were identified by immunoprecipitation with specific antisera. The translation products encoded by the glycoprotein B gene were 103,000 and 99,000 in molecular weight. The translation products encoded by the ICP8 gene were 125,000 and 122,000 in molecular weight.     

Cell-free RNA replication systems based on a human cell extracts-derived in vitro translation system with the encephalomyocarditisvirus RNA

To study the relationship between translation and replication of encephalomyocarditisvirus (EMCV) RNA, we established a cell-free RNA replication system by employing a human cell extracts-based in vitro translation system. In this system, a cis-EMCV RNA replicon encoding the Renilla luciferase (R-luc) or GFP and the viral regulatory proteins efficiently replicated with simultaneous translation of the encoded protein. To examine how translation of the replicon RNA, but not the translated products, affected replication, a trans-EMCV RNA replicon encoding R-luc and the RNA replication elements was next constructed. The trans-replicon RNA replicated only in the presence of the regulatory proteins pre-expressed in trans. Incubation with cycloheximide, puromycin or a dominant-negative eukaryotic translation initiation factor 4A following expression of the regulatory proteins almost completely inhibited not only translation of the trans-replicon RNA but also replication of the RNA, suggesting that EMCV RNA translation promotes replication of the RNA. In conclusion, the cell-free RNA replication systems should become useful tools for the study of the viral RNA replication.