Intervening polyadenylate sequences in RNA transcripts of vesicular stomatitis virus

Structures and Mechanisms of Nonsegmented, Negative-Strand RNA Virus Polymerases

The nonsegmented, negative-strand RNA viruses (nsNSVs), also known as the order Mononegavirales, have a genome consisting of a single strand of negative-sense RNA. Integral to the nsNSV replication cycle is the viral polymerase, which is responsible for transcribing the viral genome, to produce an array of capped and polyadenylated messenger RNAs, and replicating it to produce new genomes. To perform the different steps that are necessary for these processes, the nsNSV polymerases undergo a series of coordinated conformational transitions. While much is still to be learned regarding the intersection of nsNSV polymerase dynamics, structure, and function, recently published polymerase structures, combined with a history of biochemical and molecular biology studies, have provided new insights into how nsNSV polymerases function as dynamic machines. In this review, we consider each of the steps involved in nsNSV transcription and replication and suggest how these relate to solved polymerase structures.

S-adenosyl homocysteine-induced hyperpolyadenylation of vesicular stomatitis virus mRNA requires the methyltransferase activity of L protein

There are many unique aspects of vesicular stomatitis virus (VSV) transcription. In addition to its unusual mRNA capping and methyltransferase mechanisms, the addition of S-adenosyl homocysteine (SAH), which is the by-product and competitive inhibitor of S-adenosyl methionine (SAM)-mediated methyltransferase reactions, leads to synthesis of poly(A) tails on the 3' end of VSV mRNAs that are 10- or 20-fold longer than normal. The mechanism by which this occurs is not understood, since it has been shown that productive transcription is not dependent on 5' cap methylation and full-length VSV mRNAs can be synthesized in the absence of SAM. To investigate this unusual phenotype, we assayed the effects of SAH on transcription using a panel of recombinant viruses that contained mutations in domain VI of the VSV L protein. The L proteins we investigated displayed a range of 5' cap methyltransferase activities. In the present study, we show that the ability of the VSV L protein to catalyze methyl transfer correlates with its sensitivity to SAH with respect to polyadenylation, thereby indicating an intriguing connection between 5' and 3' end mRNA modifications. We also identified an L protein mutant that hyperpolyadenylates mRNA irrespective of the presence or absence of exogenous SAH. Further, the data presented here show that the wild-type L protein hyperpolyadenylates a percentage of VSV mRNAs in infected cells as well as in vitro.

Polymerase slippage at vesicular stomatitis virus gene junctions to generate poly(A) is regulated by the upstream 3'-AUAC-5' tetranucleotide: implications for the mechanism of transcription termination

Termination of mRNA synthesis in vesicular stomatitis virus (VSV), the prototypic rhabdovirus, is controlled by a 13-nucleotide gene end sequence which comprises the conserved tetranucleotide 3'-AUAC-5', the U(7) tract and the intergenic dinucleotide. mRNAs terminated at this sequence possess 100- to 300-nucleotide-long 3' poly(A) tails which are thought to result from polymerase slippage (reiterative transcription) by the VSV polymerase on the U(7) tract. Previously we determined that in addition to the AUAC tetranucleotide, the U(7) tract was an essential signal in the termination process. Shortening or interrupting the U(7) tract abolished termination. These altered U tracts also prevented the polymerase from performing reiterative transcription necessary for generation of the mRNA poly(A) tail and thus established seven residues as the minimum length of U tract that allowed reiterative transcription to occur. In this study we investigated whether sequences other than the essential U(7) tract are involved in controlling polymerase slippage. We investigated whether the AUAC tetranucleotide affected the process of reiterative transcription by analyzing the nucleotide sequence of RNAs transcribed from altered subgenomic templates and infectious VSV variants. The tetranucleotide was found to regulate reiterative transcription on the U(7) tract. The extent of polymerase slippage was governed not by specific tetranucleotide sequences but rather by nucleotide composition such that slippage occurred when the tetranucleotide was composed of A or U residues but not when it was composed of G or C residues. This suggested that polymerase slippage was controlled, at least in part, by the strength of base pairing between the template and nascent strands. Further data presented here indicate that the tetranucleotide contains both a signal that directs the VSV polymerase to slip on the downstream U(7) tract and also a signal that directs a slipping polymerase to terminate mRNA synthesis.

Polyadenylation of vesicular stomatitis virus mRNA dictates efficient transcription termination at the intercistronic gene junctions

The intercistronic gene junctions of vesicular stomatitis virus (VSV) contain conserved sequence elements that are important for polyadenylation and transcription termination of upstream transcript as well as reinitiation of transcription of downstream transcript. To examine the role of the putative polyadenylation signal 3'AUACU(7)5' at the gene junctions in polyadenylation and transcription termination, we constructed plasmids encoding antigenomic minireplicons containing one or two transcription units. In plasmid-transfected cells, analyses of the bicistronic minireplicon containing the wild-type or mutant intercistronic gene junctions for the ability to direct synthesis of polyadenylated upstream, downstream, and readthrough mRNAs showed that the AUACU(7) sequence element is required for polyadenylation of VSV mRNA. Deletion of AUAC or U(7) resulted in templates that did not support polyadenylation of upstream mRNA. Interestingly, we found that the loss of polyadenylation function led to antitermination of the upstream transcript and resulted in a readthrough transcript that contained the upstream and downstream mRNA sequences. Mutations that blocked polyadenylation also blocked transcription termination and generated mostly readthrough transcript. Reverse transcription-PCR of readthrough transcripts and subsequent nucleotide sequencing of the amplified product revealed no extra adenosine residues at the junction of the readthrough transcript. These results indicate that polyadenylation is required for transcription termination of VSV mRNA. The intergenic dinucleotide GA did not appear to be necessary for transcription termination. Furthermore, we found that insertion of the polyadenylation signal sequence AUACU(7) alone was sufficient to direct polyadenylation and efficient transcription termination at the inserted site. Taken together, the data presented here support the conclusion that polyadenylation is the major determinant of transcription termination at the intercistronic gene junctions of VSV.

cis-Acting signals involved in termination of vesicular stomatitis virus mRNA synthesis include the conserved AUAC and the U7 signal for polyadenylation

We investigated the cis-acting sequences involved in termination of vesicular stomatis virus mRNA synthesis by using bicistronic genomic analogs. All of the cis-acting signals necessary for termination reside within the first 13 nucleotides of the 23-nucleotide conserved gene junction. This 13-nucleotide termination sequence at the end of the upstream gene comprises the tetranucleotide AUAC, the tract containing seven uridines (U7 tract), and the intergenic dinucleotide (GA), but it does not include the downstream gene start sequence. Data presented here show that upstream mRNA termination is independent of downstream mRNA initiation. Alteration of any nucleotide in the 13-nucleotide sequence decreased the termination activity of the gene junction and resulted in increased synthesis of a bicistronic readthrough RNA. This finding indicated that the wild-type gene junction has evolved to achieve the maximum termination efficiency. The most critical position of the AUAC sequence was the C, which could not be altered without complete loss of mRNA termination. Reducing the length of the wild-type U7 tract to zero, five, or six U residues also totally abolished mRNA termination, resulting in exclusive synthesis of the bicistronic readthrough mRNA. Shortening the wild-type U7 tract to either five or six U residues abolished VSV polymerase slippage during readthrough RNA synthesis. Since neither the U5 nor U6 template was able to direct mRNA termination, these data imply that polymerase slippage is a prerequisite for termination. Evidence is also presented to show that in addition to causing polymerase slippage, the U7 tract itself or its poly(A) product constitutes an essential signal for mRNA termination.

Increased synthesis of polycistronic mRNA associated with increased polyadenylation by vesicular stomatitis virus

Electron microscopy suggested that the mRNA produced in vitro by tsG16(I), a temperature-sensitive mutant of vesicular stomatitis virus, contained an increased proportion of polycistronic mRNAs. Using hybrid selection, we found that the poly(A)+ mRNA synthesized in vitro by tsG16(I) contained approximately two to three times more polycistronic mRNA than did poly(A)+ mRNA synthesized in vitro by the parental wild-type (wt) virus. The increase in polycistronic mRNA occurred at all intergenic junctions examined. In vitro, tsG16(I) has an increased polyadenylation phenotype and a temperature-sensitive transcriptase activity that appear to be due to different mutations. Partial revertants of tsG16(I), which have lost the aberrant polyadenylation phenotype but retain the in vitro thermosensitive transcriptase, produced wt amounts of polycistronic mRNA. This suggested that the increased production of polycistronic mRNA by tsG16(I) may be associated with the increased polyadenylation phenotype of this mutant. These data further support the hypothesis that an increase in size of poly(A) tracts is associated with increased production of polycistronic mRNA.

Influenza A virus in vitro transcription: roles of NS1 and NP proteins in regulating RNA synthesis

To study the mechanisms by which the influenza A virus RNA-dependent RNA polymerase switches from transcription to replication we have devised a riboprobe protection technique with which we analyzed the 3' end sequence of (+)-strand RNA products of an in vitro transcription reaction containing purified virion-RNP complexes in the presence and the absence of the putative regulatory proteins NP and NS1. We found that the addition of these proteins did not result in the synthesis of full-length (+)-strand RNA products resulting from read-through of the polyadenylation signal or replication. Because NS1 and NP are both phosphoproteins we searched for protein kinase activity that might play a role in regulating RNA synthesis. We showed that virion RNP complexes phosphorylated NS1 but possessed no autophosphorylating activity. Soluble NP protein derived from RNP complexes did not phosphorylate NS1, but did phosphorylate casein. When NP protein was dephosphorylated, however, it no longer phosphorylated casein. We also showed that NS1 was an ssRNA-binding protein which binds nonspecifically to all ssRNA, and that this activity is not dependent on its state of phosphorylation.

RNA editing by G-nucleotide insertion in mumps virus P-gene mRNA transcripts

A guanine nucleotide insertion event has been shown to occur at a specific site within mumps virus P-gene mRNA transcripts. The region of the mRNA containing the site expected to be used for RNA editing and the complementary portion of the genomic RNA were cloned, and their nucleotide sequences were obtained. The genomic RNA was found to possess six C residues at the insertion site, whereas 63% of the P-gene-specific mRNA transcripts were found to have from two to five G residues inserted at this position in the RNA. An unedited mRNA was shown to encode the mumps virus cysteine-rich protein V, and mRNA transcripts containing two and four inserted G residues were translated to yield the mumps virus P and I proteins, respectively.

Molecular cloning of pneumonia virus of mice

cDNA clones representing nine genes of pneumonia virus of mice (PVM) have been generated. The sizes of the corresponding mRNAs and a provisional transcriptional map of the virus genome have been determined. The apparent gene order is very similar to that of respiratory syncytial virus. The sequences adjacent to the 3' termini of the PVM genes were determined and are very similar to those of respiratory syncytial virus. Several PVM gene polypeptide products have been assigned.

Structure and function of bicistronic RNA encoding the phosphoprotein and matrix protein of measles virus

Two independent full-length replicas of a bicistronic RNA species containing the complete P and M genes of measles virus arranged in tandem were isolated from an expressible cDNA library. Sequences at the 5' and 3' termini suggested that the bicistronic RNA was initiated and terminated at precisely the same locations as the monocistronic mRNAs of the P and M genes, respectively. The P and M cistrons were fused together via an intergenic region which was exactly colinear with and complementary to the intergenic region of the genomic RNA. This RNA species was polyadenylated at the normal polyadenylation site at the 3' terminus of the M cistron, but not in the intergenic region. By DNA-mediated gene transfer, these cDNA clones were expressed into bicistronic RNA containing both P and M sequences in primate cells. RNA thus generated did not undergo nucleolytic processing but was translated into high levels of a 70,000-Mr protein immunoprecipitated by monoclonal antiserum against the measles virus P protein. M protein was not produced in the same cells even though the M cistron could direct M protein synthesis in vitro once excised from the upstream P cistron. These results suggested that bicistronic RNA could direct protein synthesis from the first but not the second cistron and might contribute at least in part to expression of viral genes in vivo.

Processing of phage T4 td-encoded RNA is analogous to the eukaryotic group I splicing pathway

Several features of the split td gene of phage T4 suggest an RNA processing mechanism analogous to that of the self-splicing rRNA of Tetrahymena and other group I eukaryotic introns. Previous work has revealed conserved sequence elements and the ability of td-encoded RNA to self-splice in vitro. We show here that a noncoded guanosine residue is covalently joined to the 5' end of the intron during processing. Further, we demonstrate the existence of linear and circular intron forms in RNA extracted from T4-infected cells and from uninfected Escherichia coli expressing the cloned td gene. Sequence analysis of the intron cyclization junction indicates that the noncoded guanosine and one additional nucleotide are lost from the 5' end of the intron upon cyclization. This analysis places a uridine residue upstream of the cyclization site, in analogy to three other group I cyclization junctions. These striking similarities to the splicing intermediates of eukaryotic group I introns point not only to an analogous processing pathway and conserved features of cyclization site recognition but also to a common ancestry between this prokaryotic intervening sequence and the group I eukaryotic introns.

Identification of the sequence content of four polycistronic transcripts synthesized in Newcastle disease virus infected cells

During infection, the Newcastle disease virus (NDV) genome is transcribed to produce 5 to 7 species of polycistronic messenger RNA (Wilde and Morrison, J. Virol. 51, 71-76) in addition to the well characterized monocistronic messenger RNA. To identify the specific sequences present in each of the polycistronic RNA species, cDNA clones generated by reverse transcription of NDV mRNAs were characterized and used as probes on Northern blots of total NDV cytoplasmic RNA. By this method, it was shown that four of these large RNA species are polycistronic transcripts containing sequences from two genes: one species contains nucleocapsid protein (NP) and phosphoprotein (P) gene sequences; another, P and membrane protein (M) gene sequences; another, M and fusion protein (F0) gene sequences; and another, F0 and hemagglutinin-neuraminidase protein (HN) gene sequences. The existence of these transcripts yields a transcription map order of NP, P, M, F0, HN. The remaining RNA bands may be composed of at least three different polycistronic transcripts, each of which represents transcription through three adjacent genes.

Correct sequence for the major nucleocapsid protein mRNA of respiratory syncytial virus

A nucleotide sequence for the mRNA of the major nucleocapsid (N) protein gene of respiratory syncytial virus was reported previously (N. Elango and S. Venkatesen, 1983, Nucleic Acids Res. 11, 5941-5951). However, we have been unable to confirm part of this sequence as N mRNA-specific and suggest that the published sequence represents that of an aberrant chimeric transcript. Here we present an alternative sequence for the N mRNA and provide data supporting its authenticity. The corrected N mRNA sequence contains 1197 rather than 1427 nucleotides exclusive of poly(A), and encodes a protein of 391 rather than 467 amino acids. The calculated molecular weight for the 391-amino acid protein described by the sequence presented here is 42,600, in agreement with the molecular weight of 42,000 determined for the RS viral N protein by gel electrophoresis. In addition, we present sequence data from dicistronic RNAs that span the junction between the 1B protein and N cistrons, and the junction between the N and phosphoprotein (P) cistrons.

Nucleotide sequences of the 1B and 1C nonstructural protein mRNAs of human respiratory syncytial virus

The genes encoding the 1C and 1B mRNAs of human respiratory syncytial (RS) virus are first in the order of viral transcription and encode nonstructural (NS) proteins of approximate molecular weights 14,000 and 11,000, respectively, estimated by gel electrophoresis. The complete nucleotide sequences of the 1C and 1B mRNAs determined from several full-length cDNA clones are described. The 1C and 1B mRNAs contain 528 and 499 nucleotides, respectively, exclusive of poly(A), and encode proteins of 139 and 124 amino acids. The calculated molecular weights of the predicted NS1C and NS1B proteins are 15,567 and 14,674, respectively. Both mRNA sequences contain the 5'-terminal sequence, 5' GGGGCAAAU . . . , and the 3'-terminal sequence, 5' . . . AGUAUA(N)1-4-poly(A), that were identified previously as conserved among six other RS viral mRNAs. In addition, a dicistronic readthrough RNA having the general structure 5' 1C mRNA-intergenic sequence-1B mRNA 3' was identified by dideoxynucleotide sequencing of intracellular poly(A)+ RNA using a DNA primer derived from a 1B-cDNA clone. In the dicistronic RNA, the nucleotide sequences of the 1C and 1B cistrons are separated by, in mRNA sense, four A residues and the intergenic sequence 5' . . . CUUAACAGAAGACAAAAAN . . . 3' (N represents unidentified nucleotide). The significance of these sequences is discussed.

The envelope-associated 22K protein of human respiratory syncytial virus: nucleotide sequence of the mRNA and a related polytranscript

We recently determined that respiratory syncytial virus (strain A2) encodes a fourth unique envelope-associated virion protein that has molecular weight of approximately 24,000, as estimated by gel electrophoresis. The nucleotide sequence of the mRNA encoding this novel protein has now been determined from five cDNA clones, including three that contain the complete mRNA sequence. The complete mRNA sequence is 957 nucleotides, exclusive of polyadenylate, and contains two partially overlapping open reading frames. The 5'-proximal open reading frame is favored for utilization by the criteria of the location and sequence of its translational start site. Furthermore, the calculated molecular weight of the encoded protein, 22,153, is in agreement with the previous estimate of 24,000 for the authentic protein identified by hybrid selection and in vitro translation. The sequence of the predicted protein, now designated the 22K protein, contains 194 amino acids, is relatively hydrophilic, and appears to be the most basic of the respiratory syncytial virus proteins. The mRNA also contains a second, internal open reading frame which would encode a protein of 90 amino acids. However, no evidence for this translation product is known. The first nine nucleotides in the mRNA sequence, 5'-GGGGCAAAU, are identical to the conserved sequence identified previously at the 5' termini of seven other respiratory syncytial viral mRNAs; the sequence at the 3' end of the 22K mRNA, 5'. . . AGUUAUUU-polyadenylate, contains the elements of the previously identified 3'-terminal consensus sequence for respiratory syncytial virus mRNAs, AGUUAA(N)1-4-polyadenylate (P. L. Collins, Y. T. Huang, and G. W. Wertz, Proc. Natl. Acad. Sci. U.S.A. 81:7683-7687). In addition, we present and describe the intergenic sequence of a dicistronic RNA derived from readthrough of the F and 22K protein genes.

Use of antibodies directed against synthetic peptides for identifying cDNA clones, establishing reading frames, and deducing the gene order of measles virus

A number of cDNA clones complementary to measles virus mRNA and 50S genome RNA have been generated. These clones have been mapped by restriction enzyme analysis and were subsequently sequenced by the method of Maxam and Gilbert (A. M. Maxam and W. Gilbert, Methods Enzymol. 65:499-560, 1980). Computer analysis of these DNA sequences revealed open reading frames which potentially could code for a number of gene products. Portions of these putative polypeptides were synthesized, and rabbit antibodies directed against peptide-hemocyanin conjugates were produced. These antibodies were used to immunoprecipitate virus-specific polypeptides which were identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. For each of the antisera tested, a unique protein was precipitated whose migration on polyacrylamide gels corresponded to standard gene products identified by monoclonal antibodies and antisera against measles virus. By using this method, we were able to assign the coding regions of cDNA clones to specific protein products and, subsequently, to order the genes of the 3'-terminal third of measles genome RNA.

Polytranscripts of Sendai virus do not contain intervening polyadenylate sequences

Discrete high-molecular-weight RNA species with the properties of polytranscripts were observed in poly(A)-rich RNA extracted from Sendai virus-infected cells. These RNA species were virus specific, being synthesized in the presence of actinomycin D, but not seen in uninfected cells. They were not genome or antigenome fragments, since they were not encapsidated, as shown by their destruction when ribonuclease was added to cell homogenates and by their absence from the RNA fractions that did not bind to oligo(dT)-cellulose. Two lines of evidence indicated that the gene-specific regions of these polytranscripts were not linked by poly(A) sequences, but were faithful copies of virus genomic RNA sequences at gene boundaries. First, a small cDNA clone obtained by reverse transcription of poly(A)-rich RNA species from infected cells contained 90 bases from the 5' terminus of the gene for the P protein and about 600 bases from the 3' end of the downstream gene, which specifies the M protein, the entire cloned sequence being an accurate complement of the genomic RNA. Second, dideoxynucleotide sequencing of poly(A)-rich RNA species primed by virus gene-specific oligodeoxynucleotides revealed read-through products of transcription containing no detectable poly(A). If Sendai virus polytranscripts are intermediates in the production of monocistronic viral mRNAs by a cleavage process, and poly(A) sequences do not link the mRNAs, polyadenylation would have to follow the cleavage step; it seems more likely that these polytranscipts are aberrant transcription products generated by occasional termination failure in a stop-start mechanism of transcription.

Analysis and gene assignment of mRNAs of a paramyxovirus, simian virus 5

Polypeptides synthesized by the paramyxovirus SV5 in infected CV-1 cells were readily identified when the host cell was treated with actinomycin D. The unglycosylated forms of HN and Fo synthesized in infected cells in the presence of tunicamycin and HN and Fo synthesized in vitro were identified by immunoprecipitation with specific antibodies. Separation of SV5-specific poly(A)-containing RNAs on methyl-mercury agarose gels and in vitro translation of fractions, indicated that the viral polypeptides were translated from individual mRNAs except P (Mr approximately 44K) and the nonstructural polypeptide V (Mr approximately 24K) for which the mRNAs could not be separated. cDNA copies of SV5-specific mRNAs were synthesized and cloned in plasmid pBR322. Clones to NP, P + V, M, F, and HN were identified by hybrid-arrest and hybrid-selection translation of SV5 mRNAs. Tryptic peptide mapping of polypeptides P and V indicated that the peptides of V were a subset of those of P. Hybridization of cDNA probes to infected cell mRNAs separated on agarose gels permitted identification of the NP, P + V, M, F, and HN mRNAs and presumptive polycistronic mRNAs. The sizes and sequence homologies of these polycistronic mRNAs were used to derive a likely gene order on the SV5 50 S genome RNA.

Transcriptional mapping of human respiratory syncytial virus

A transcriptional map for human respiratory syncytial virus was determined by measuring the kinetics of viral gene inactivation in response to UV irradiation. Monolayer cell cultures of respiratory syncytial virus-infected HEp-2 cells were exposed to UV light, and residual viral RNA synthesis was monitored both by gel electrophoresis and by hybridization to dot blots of cloned cDNAs of the 10 known viral genes. Target sizes for the 10 individual viral genes were calculated relative to the UV sensitivity of intracellular viral genome replication. Target size analysis indicated that the 10 viral genes were transcribed as a single transcriptional unit and that the transcription of an individual gene was dependent on the prior transcription of all the preceding genes. The order of gene transcription (with nomenclature according to encoded proteins) was determined to proceed from the promoter as follows: 14K, 11K, N, P, M, 9.5K, 36K, F, 24K, L.

Measles virus gene expression in subacute sclerosing panencephalitis

RNA was extracted from the diseased brain of a case of human subacute sclerosing panencephalitis (SSPE) and analysed for the expression of measles-specific RNA. Measles virus-specific mRNAs were present, but the amount of matrix (M) protein mRNA was greatly reduced in comparison to lytically infected cells and phospho- (P) protein mRNA was hardly detectable whereas the level of the corresponding intermediate-sized (is-) RNA was greatly increased. RNA obtained from the human brain was also translated in vitro and measles virus nucleocapsid and P protein was produced. However, in marked contrast to control reactions M protein was not detected in the products formed by translation in vitro. These results indicate an impaired measles virus M protein mRNA synthesis in infected brain tissue.

Structural and functional characterization of Newcastle disease virus polycistronic RNA species

Upon infection, the Newcastle disease virus (NDV) genome is transcribed to produce 18S, 22S, and 35S RNAs (M. Bratt , and W. Robinson, J. Mol. Biol. 23:1-21, 1967). The 22S RNA has been shown to contain 18S sequences and is thought to represent polycistronic transcripts generated by transcriptional readthrough of adjacent genes ( Varich et al., Acta Virol. 23:341-343, 1979). With improved extraction procedures, the 22S RNA was found to represent up to 25% of the total transcription in NDV-infected cells. This RNA was resolved into at least five discrete species on formaldehyde-agarose gels. All but one of these molecules contain 3' polyadenylate sequences but not internal polyadenylate sequences. These transcripts are found on polyribosomes of infected cells, suggesting that they are functional mRNAs.

Nucleotide sequence of an aberrant glycoprotein mRNA synthesized by the internal deletion mutant of vesicular stomatitis virus

The transcriptionally active internal deletion mutant (DI-LT) of vesicular stomatitis virus synthesizes an abnormal mRNA (G*) containing a transcript of the remnant polymerase gene covalently linked to the 3' end of the glycoprotein message (R.C. Herman and R.A. Lazzarini, J. Virol. 40:78-86, 1981). A complementary DNA copy of the 3' end of the G* transcript was molecularly cloned and then chemically sequenced. The results showed that the deletion removed the last 54 nucleotides of the normal glycoprotein gene, the intergenic dinucleotide, and all but the last 258 nucleotides of the polymerase gene. The sequence of DI-LT at the deletion site was compared to that of the transcriptionally inactive DI-LT2 particle.

Detection of in vivo synthesis of polycistronic mRNAs of vesicular stomatitis virus

The in vivo synthesis of polycistronic transcripts of vesicular stomatitis virus in human amnion U cells and mouse L cells was detected by RNA blot hybridization. Within the molecular weight range resolved by this gel electrophoresis system, all possible combinations of sequentially linked messages were observed, as identified by their patterns of hybridization and their apparent molecular weights. Actinomycin D pretreatment of mouse L cells did not affect the frequency or size of polycistronic messages, nor did these differ between L cells and U cells. Vesicular stomatitis virus polycistronic transcripts were synthesized in vivo in a roughly uniform distribution, except for the NS-M dicistronic mRNA, which was much more frequent. Most of the polycistronic RNA species were found to be poly(A)+, but at least one, the tetracistronic molecule N-NS-M-G, was clearly poly(A)-. Analysis of RNA following treatment with RNase H in the presence of oligo(dT) indicated that the in vivo-synthesized poly(A)+ polycistronic species NS-M, M-G, and N-NS-M had poly(A) tracts at their 3' molecular termini but not internally at their intercistronic junctions.

Identification of a tenth mRNA of respiratory syncytial virus and assignment of polypeptides to the 10 viral genes

Nine mRNAs, their cDNA clones, and a genome transcriptional map have been reported previously for respiratory syncytial virus (P. L. Collins and G. W. Wertz, Proc. Natl. Acad. Sci. U.S.A. 80:3208-3212, 1983). We report here the identification of a 10th viral mRNA, designated mRNA 2b (molecular weight [MW] ca. 0.39 X 10(6)), that was detected by RNA (Northern) blot hybridization with cDNA clones. Analysis of a polycistronic readthrough transcript was used to deduce the position in the viral transcriptional map of the gene encoding the newly identified mRNA. The polypeptide coding assignments of 9 of the 10 respiratory syncytial virus mRNAs were determined. Individual viral mRNAs were purified by hybridization selection with nine unique, nonoverlapping cDNA clones and analyzed by translation in vitro. Each of the nine mRNAs encoded a single polypeptide chain. The coding assignments were as follows: RNA 1a (MW ca. 0.24 X 10(6)), a 9,500-dalton (9.5K) protein; RNA 1b (MW 0.26 X 10(6)), an 11K protein; RNA 1c (MW 0.26 X 10(6)), a 14K protein; RNA 2a (MW 0.38 X 10(6)), the 34K phosphorylated (P) protein; RNA 2b (MW 0.39 X 10(6)), a 36K protein; RNA 3a (MW 0.40 X 10(6)), the 26K matrix (M) protein; RNA 3b (MW 0.40 X 10(6)), a 24K protein; RNA 4 (MW 0.47 X 10(6)), the 42K major nucleocapsid (N) protein; and RNA 5 (MW 0.74 X 10(6)), a 59K protein. The cDNA clones used for the hybridization selections were respiratory syncytial virus specific and did not hybridize with uninfected-cell mRNA; therefore the proteins synthesized with the selected mRNAs were virus specific. The 9.5K, 11K, 14K, 24K, M, P, 36K, N, and 59K proteins were encoded by different mRNAs; therefore these nine proteins are all unique. The 9.5K, 11K, 14K, 24K, M, P, and N proteins synthesized in vitro with hybrid-selected mRNAs each had counterparts with the same electrophoretic mobilities in extracts of virus-infected cells. The in vitro polypeptides and their authentic counterparts were shown to be closely related by limited digest peptide mapping. The 36K and 59K polypeptides lacked counterparts with the same electrophoretic mobilities in infected cells and therefore are candidates for the unprocessed precursors of the viral F and G glycoproteins. The 10th viral mRNA, the 2,500K RNA 7, was not tested directly but is the only known mRNA of the appropriate size to encode the 200K large (L) protein of the viral nucleocapsid. These assignments account for all 10 of the reported viral mRNAs and bring to 10 the number of known unique viral proteins.

Initiation of RNA synthesis in vitro by vesicular stomatitis virus: single internal initiation in the presence of aurintricarboxylic acid and vanadyl ribonucleoside complexes

In the presence of aurintricarboxylic acid (ATA) and vanadyl ribonucleoside complexes (VRC), we have isolated and characterized a small RNA, product of VSV in vitro transcription. This RNA is capped and lacks poly(A) at its 3'-end. Nucleotide sequence analysis revealed that this RNA corresponds to the 5'-terminal transcription product of the N-gene. The termination of the transcription occurs precisely at the 118th base from the 3'-end of the VSV genome. Analysis of the nucleotide sequence around this region reveals a potential secondary structure. Photoreaction of the VSV with 4'-substituted psoralen fails to inhibit the synthesis of the 68-mer RNA under conditions where full length mRNA synthesis is blocked, indicating that the psoralen binding site is located further into the N-gene. Since this RNA is the only in vitro transcription product synthesized under these conditions, the existence of two types of polymerase activities, one for the synthesis of leader RNA and one for mRNA, is suggested.

Conditional synthesis of an aberrant glycoprotein mRNA by the internal deletion mutant of vesicular stomatitis virus

The internal deletion mutant (DI-LT) derived from the heat-resistant strain of vesicular stomatitis virus synthesizes an aberrant polyadenylated mRNA (G*) containing a transcript of the partially deleted polymerase gene covalently linked to the 3' end of the glycoprotein message (R. C. Herman and R. A. Lazzarini, J. Virol. 40:78-86, 1981). The heat-resistant polymerase appears to play a role in the synthesis of the abnormal G* RNA. The synthesis of G* correlated directly with the presence of the heat-resistant L protein on the defective interfering particle template. Chimeric defective interfering particles produced by passaging DI-LT with a helper virus that encodes the wild-type vesicular stomatitis virus polymerase did not synthesize G*. The subsequent passage of the chimeric DI-LT with a heat-resistant helper virus restored the ability to synthesize the G* transcript. These results imply that the regulatory signals normally present at the vesicular stomatitis virus G/L intercistronic boundary may be preserved in DI-LT. These sequences are only conditionally functional because they are recognized correctly by the wild-type but not by the heat-resistant polymerase.

Vesicular stomatitis virus mutant with altered polyadenylic acid polymerase activity in vitro

In vitro RNA synthesis by purified virions of a stock of tsG16(I) was aberrant compared with that of wild-type (wt) vesicular stomatitis virus. RNA made in vitro by tsG16(I) contained a larger proportion of A residues in polyadenylic acid [poly(A)] tracts than did RNA synthesized by wt virus, tsG13(I), tsG21(II) or tsG41(IV). Experiments to determine whether the aberrant polyadenylation was correlated with the known thermolability of the tsG16(I) L protein were inconclusive. Total product RNA made by tsG16(I) was methylated to almost the same extent as wt RNA, contained the same major methylated 5' cap structure as wt RNA, and was translated as well in a reticulocyte cell-free system, yielding the same molecular weight proteins in similar ratios. Most polyadenylated [poly(A)+] RNA made by tsG16(I) was considerably larger than wt poly(A)+ RNA and richer in AMP:UMP residues; however, the protein-coding capacities of mutant and wt poly(A)+ RNAs were similar. This suggested that most mRNAs made in vitro by tsG16(I) might possess very long poly(A)+ tracts, and digestion of RNA by T1 RNase supported this. It appeared, therefore, that a virally coded component of vesicular stomatitis virus could affect polyadenylation. This could be the poly(A) polymerase itself, a protein involved in control of polyadenylation, or a protein which affects an event spatially and temporally connected with polyadenylation (such as initiation of the subsequent mRNA).

cDNA cloning and transcriptional mapping of nine polyadenylylated RNAs encoded by the genome of human respiratory syncytial virus

We have isolated cDNA clones representing nine unique poly(A)+ RNAs transcribed from the genome of human respiratory syncytial virus, a paramyxovirus. A cDNA library was constructed by using poly(A)+ RNA from virus-infected cells as template and the Escherichia coli plasmid pBR322 as vector. Viral cDNA clones were identified by hybridization with cDNA probes prepared from viral genomic RNA. The viral clones were grouped into nine different families by hybridization with individual size-selected reverse transcripts representing the major classes of poly(A)+ RNA from virus-infected cells. The largest clone from each family was selected for analysis. These nine clones, molecular sizes ranging from 520 to 2,600 base pairs, were shown to be unrelated on the basis of reciprocal hybridization using dot-blots. These cDNA clones were then used as hybridization probes to analyze intracellular viral RNAs that had been separated by gel electrophoresis and transferred to diazobenzyloxymethyl-paper. All nine clones hybridized with intracellular viral genomic RNA, confirmation of virus specificity. Nine unique intracellular viral poly(A)+ RNAs were identified [molecular sizes ranging from 720 to 7,500 nucleotides, including poly(A)]. Comparison of the sizes of these major RNAs and the cDNA clones indicated that a number of the clones represented nearly complete copies of the corresponding RNAs. Several other intracellular viral poly(A)+ RNAs appeared to be polycistronic by the criteria of molecular weights and homologies to various combinations of cDNA clones. The sizes and sequence contents of these polycistronic RNAs were used to prepare a transcriptional map whose significance is discussed.

Identification and characterization of a group of discrete initiated oligonucleotides transcribed in vitro from the 3' terminus of the N-gene of vesicular stomatitis virus

Four triphosphate-initiated oligonucleotides, 11 to 14 bases long, produced by in vitro transcription of vesicular stomatitis virus were identified as the uncapped 5' sequences of N-gene mRNA. Characterization of these oligonucleotides reveals that they are continually produced stable transcripts that do not remain template bound. Under the conditions used, the oligonucleotide transcripts were produced at 8 to 10 times the molar amount of leader, suggesting that the N-gene mRNA is internally initiated.

Aberrant glycoprotein mRNA synthesized by the internal deletion mutant of vesicular stomatitis virus

The internal deletion mutant (DI-LT) derived from the heat-resistant strain of vesicular stomatitis virus synthesized an aberrant polyadenylated mRNA in vivo and in vitro. No normal glycoprotein message could be detected among the in vivo transcription products. The abnormal RNA contained a transcript of the partially deleted polymerase gene covalently linked to the 3' end of the glycoprotein message. The polyadenylate is located at the 3' end of the molecule and is most probably encoded by the remnant polymerase gene polyadenylation signal. This aberrant RNA may be synthesized because of either a failure to terminate transcription at the end of the glycoprotein gene or an inability to process an abnormal polycistronic precursor.

Synthesis of capped and uncapped methylated oligonucleotides by the virion transcriptase of spring viremia of carp virus, a rhabdovirus

Capped and uncapped methylated oligonucleotides, five and six nucleotides in length, were synthesized in vitro in spring viremia of carp virus transcription reaction mixtures containing ATP + CTP, ATP + CTP + GTP, or ATP + CTP + UTP, but not in any other combinations of two or three ribonucleoside triphosphates. The oligonucleotides that have been characterized are consistent with the structures: m7GpppAmpNpCpNpN, GpppAmpNpCpNpN, pppAmpNpCpNpN, and ppAmpNpCpNpN--i.e., similar to those of the termini of transcripts made in complete reaction mixtures. Because both capped and uncapped methylated oligonucleotides were synthesized, it can be concluded that methylation of the penultimate nucleotide can precede capping and methylation of the capping nucleotide. Our results also indicate that capping and methylation are processes that can take place prior to mRNA chain completion.

In vivo transcription of the 5'-terminal extracistronic region of vesicular stomatitis virus RNA

In vivo transcription and polyadenylation at the junction of the L cistron and the 5'-terminal extracistronic region of vesicular stomatitis virus RNA was investigated. Annealing of 5'32P-labeled RNA representing the 5'-terminal noncoding 77 nucleotides of vesicular stomatitis virus genomic RNA to L gene mRNA resulted in specific duplex formation. Two specific RNase T1- and RNase A resistant duplexes, 66 and 77 nucleotides long, bound to oligodeoxythymidylic acid cellulose. The specific sizes of the duplexes and their selection by oligodeoxythymidylic acid cellulose chromatography demonstrated that they were covalently linked to the polyadenylic acid tail of L gene mRNA. These data strongly suggest that the viral polymerase polyadenylates L gene mRNA in vivo by using the stretch of seven uridine residues at the end of the L cistron and that the polymerase can resume transcribing the 5'-terminal extracistronic region, resulting in a covalent linkage of the transcript to the polyadenylic acid tail of L gene mRNA.

Localized attenuation and discontinuous synthesis during vesicular stomatitis virus transcription

We have analyzed the process of partial transcription termination (attenuation), which results in nonequimolar synthesis of vesicular stomatitis virus (VSV) mRNAs during sequential transcription. Comparison of the level of transcription of defined regions of the VSV genome by DNA-RNA hybridization shows that attenuation occurs at or near the intergenic regions, rather than nonspecifically throughout the genome. Transcription decreases 29-33% across the junctions of the N-NS, NS-M and M-G genes, resulting in a cumulative effect on gene expression. This is the first example of a site-specific attenuation mechanism in a eucaryotic system. Analysis of the kinetics of transcription in vitro shows that transcription appears to be discontinuous, with significant pauses (2.5-5.7 min) occurring at or near the intergenic regions. Such pauses may occur during polyadenylation by a "slippage" mechanism at the U7 sequences present at each gene junction, or may be due to some other process, such as initiation or capping, which is slow relative to transcription.

Transcriptional map for Newcastle disease virus

A transcriptional map of Newcastle disease virus was determined by measuring the kinetics of UV inactivation of the transcription of individual genes and of viral infectivity. The inactivation of single genes was monitored by measuring the reduction in the accumulation of viral gene products in vivo and in vitro. In vivo, the accumulation of viral polypeptides in infected cells was measured after reversal of a cycloheximide treatment designed to inhibit secondary transcription. Actinomycin D and a hypertonic medium were used to decrease selectively the synthesis of host cell polypeptides in infected cells. In vitro, mRNA's synthesized by irradiated viruses were analyzed by translation in cell-free systems under conditions in which the amount of each polypeptide synthesized reflected the relative abundance of the corresponding mRNA. UV target sizes were obtained for the genes coding for the HN, F0, NP, M, L, and P polypeptides; the 47,000-dalton protein was not detected. A comparison of the UV target sizes with the corresponding gene sizes suggested that transcription of these genes initiated at a single promotor and proceeded in the order NP, P, (F0, M), HN, L. These experiments were performed with Newcastle disease virus strains Australia-Victoria and B1-Hitchner; for both strains, two forms of the P polypeptide which differed in electrophoretic mobility were detected. Proof that the P protein is virus specific was obtained. In addition, infection of chicken embryo cells with avirulent strain B1-Hitchner enhanced the accumulation of at least four polypeptides that appeared to be specified by the host cell rather than by the infecting virus.

Polycistronic vesicular stomatitis virus RNA transcripts

A procedure to enrich for the sequences present at the junction between the linked messages in the polycistronic RNAs symthesized in vitro by vesicular stomatitis virus (VSV) is described. Analyses of these sequences show that they contain a precise transcript of both the intercistronic dinucleotide and the pentanucleotide 5'--C-U-G-U-U--3', common to the 5'-end of all VSV cistrons, covalently linked to the 3'-side of the intervening poly(A). The data strongly suggest that the VSV transcriptase polyadenylylates the mRNAs and can then resume direct and precise transcription of the genome-without reinitiation and without skipping nucleotides.

Site on the vesicular stomatitis virus genome specifying polyadenylation and the end of the L gene mRNA

The 5'-terminal nucleotide sequence from positions 50 to 130 of vesicular stomatitis virus RNA was determined indirectly by using a defective interfering particle RNA which contains covalently linked genomic minus and antigenomic plus sense RNAs. The last 18 nucleotides of the L gene coding for in the viral polymerase were identified and isolated by specific duplex formation between 5' terminally labeled oligonucleotides from a small single-stranded defective interfering particle RNA and L gene mRNA. The L gene ends at position 60 from the 5' terminus of the vesicular stomatitis genome. The data demonstrated that the first seven adenine residues in the polyadenylic acid tail of L gene mRNA may be coded for in the genome and suggested that the viral transcriptase itself may carry out polyadenylation, possibly by chattering at the uridine-rich sequence at the end of the L gene. Analysis of the 5'-terminal sequence of vesicular stomatitis virus genomic RNA revealed that it might fold into a complex secondary structure with possibly 62% of the bases paired.

Intervening sequence between the leader region and the nucleopcapsid gene of vesicular stomatitis virus RNA

The base sequence at the 3' end of vesicular stomatitis virus RNA was determined by using terminal labels and chemical RNA sequencing. The leader RNA was complementary to 47 bases at the 3' terminus, whereas the nucleocapsid gene (N) began 51 nucleotides from the 3' end of the genomic RNA. The intervening bases were 3'...GAAA...5' for the Indiana serotype and 3'...GAAAA...5' for the New Jersey serotype. The complements of these bases did not appear in either the leader RNA or the N mRNA. This sequence may function as a stop signal or cleavage site during transcription. Furthermore, processing or termination at this sequence must be inhibited during the production of full-length RNA plus-sense strands (replication). We recently found similar sequences approximately 46 to 48 nucleotides from the 3' ends of several defective interfering particle RNAs where the short defective interfering particle transciption products terminate. This sequence is present also at the end of the polymerase (L) gene.