Initiation of translation directed by 42S and 26S RNAs from Semliki Forest virus in vitro

Entry receptors - the gateway to alphavirus infection

Alphaviruses are enveloped, insect-transmitted, positive-sense RNA viruses that infect humans and other animals and cause a range of clinical manifestations, including arthritis, musculoskeletal disease, meningitis, encephalitis, and death. Over the past four years, aided by CRISPR/Cas9-based genetic screening approaches, intensive research efforts have focused on identifying entry receptors for alphaviruses to better understand the basis for cellular and species tropism. Herein, we review approaches to alphavirus receptor identification and how these were used for discovery. The identification of new receptors advances our understanding of viral pathogenesis, tropism, and evolution and is expected to contribute to the development of novel strategies for prevention and treatment of alphavirus infection.

Mayaro Virus: The State-of-the-Art for Antiviral Drug Development

Mayaro virus is an emerging arbovirus that causes nonspecific febrile illness or arthralgia syndromes similar to the Chikungunya virus, a virus closely related from the Togaviridae family. MAYV outbreaks occur more frequently in the northern and central-western states of Brazil; however, in recent years, virus circulation has been spreading to other regions. Due to the undifferentiated initial clinical symptoms between MAYV and other endemic pathogenic arboviruses with geographic overlapping, identification of patients infected by MAYV might be underreported. Additionally, the lack of specific prophylactic approaches or antiviral drugs limits the pharmacological management of patients to treat symptoms like pain and inflammation, as is the case with most pathogenic alphaviruses. In this context, this review aims to present the state-of-the-art regarding the screening and development of compounds/molecules which may present anti-MAYV activity and infection inhibition.

Alphavirus-Induced Membrane Rearrangements during Replication, Assembly, and Budding

Alphaviruses are arthropod-borne viruses mainly transmitted by hematophagous insects that cause moderate to fatal disease in humans and other animals. Currently, there are no approved vaccines or antivirals to mitigate alphavirus infections. In this review, we summarize the current knowledge of alphavirus-induced structures and their functions in infected cells. Throughout their lifecycle, alphaviruses induce several structural modifications, including replication spherules, type I and type II cytopathic vacuoles, and filopodial extensions. Type I cytopathic vacuoles are replication-induced structures containing replication spherules that are sites of RNA replication on the endosomal and lysosomal limiting membrane. Type II cytopathic vacuoles are assembly induced structures that originate from the Golgi apparatus. Filopodial extensions are induced at the plasma membrane and are involved in budding and cell-to-cell transport of virions. This review provides an overview of the viral and host factors involved in the biogenesis and function of these virus-induced structures. Understanding virus-host interactions in infected cells will lead to the identification of new targets for antiviral discovery.

Fundamentals of Viruses and Their Proteases

Viruses are major pathogenic agents that can cause a variety of diseases, such as AIDS, hepatitis, respiratory diseases, and many more, in humans, plants, and animals. The most prominent of them have been adenoviruses, alphaviruses, flaviviruses, hepatitis C virus, herpesviruses, human immunodeficiency virus of type 1, and picornaviruses. This chapter presents an introductory remark on such viruses, mechanisms of their invasion, and diseases related to them. The inhibition of these viruses is of great concern to human beings. Each of these viruses encodes one or more proteases that play crucial roles in their replication, and thus they are important targets for the design and development of potent antiviral agents. The chapter, therefore, also introduces the readers to such proteases and their structures and functions. This chapter is thus a prelude to the remaining chapters in the book, which present in detail about the different viruses and their proteases.

Replication of alphaviruses: a review on the entry process of alphaviruses into cells

Alphaviruses are small, enveloped viruses, ~70 nm in diameter, containing a single-stranded, positive-sense, RNA genome. Viruses belonging to this genus are predominantly arthropod-borne viruses, known to cause disease in humans. Their potential threat to human health was most recently exemplified by the 2005 Chikungunya virus outbreak in La Reunion, highlighting the necessity to understand events in the life-cycle of these medically important human pathogens. The replication and propagation of viruses is dependent on entry into permissive cells. Viral entry is initiated by attachment of virions to cells, leading to internalization, and uncoating to release genetic material for replication and propagation. Studies on alphaviruses have revealed entry via a receptor-mediated, endocytic pathway. In this paper, the different stages of alphavirus entry are examined, with examples from Semliki Forest virus, Sindbis virus, Chikungunya virus, and Venezuelan equine encephalitis virus described.

Pushing the limits of the scanning mechanism for initiation of translation

Selection of the translational initiation site in most eukaryotic mRNAs appears to occur via a scanning mechanism which predicts that proximity to the 5' end plays a dominant role in identifying the start codon. This "position effect" is seen in cases where a mutation creates an AUG codon upstream from the normal start site and translation shifts to the upstream site. The position effect is evident also in cases where a silent internal AUG codon is activated upon being relocated closer to the 5' end. Two mechanisms for escaping the first-AUG rule--reinitiation and context-dependent leaky scanning--enable downstream AUG codons to be accessed in some mRNAs. Although these mechanisms are not new, many new examples of their use have emerged. Via these escape pathways, the scanning mechanism operates even in extreme cases, such as a plant virus mRNA in which translation initiates from three start sites over a distance of 900 nt. This depends on careful structural arrangements, however, which are rarely present in cellular mRNAs. Understanding the rules for initiation of translation enables understanding of human diseases in which the expression of a critical gene is reduced by mutations that add upstream AUG codons or change the context around the AUG(START) codon. The opposite problem occurs in the case of hereditary thrombocythemia: translational efficiency is increased by mutations that remove or restructure a small upstream open reading frame in thrombopoietin mRNA, and the resulting overproduction of the cytokine causes the disease. This and other examples support the idea that 5' leader sequences are sometimes structured deliberately in a way that constrains scanning in order to prevent harmful overproduction of potent regulatory proteins. The accumulated evidence reveals how the scanning mechanism dictates the pattern of transcription--forcing production of monocistronic mRNAs--and the pattern of translation of eukaryotic cellular and viral genes.

Functions of alphavirus nonstructural proteins in RNA replication

Alphaviruses are enveloped positive-strand RNA viruses transmitted to vertebrate hosts by mosquitoes. Several alphaviruses are pathogenic to humans or domestic animals, causing serious central nervous system infections or milder infections, for example, arthritis, rash, and fever. The structure and replication of Semliki Forest virus (SFV) and Sindbis virus (SIN) have been studied extensively during the past 30 years. Alphaviruses have been important probes in cell biology to study the translation, glycosylation, folding, and transport of membrane glycoproteins, as well as endocytosis and membrane fusion mechanisms. A new organelle, the intermediate compartment, operating between the endoplasmic retieulum and the Golgi complex has been found by the aid of SFV. During the past 10 years, alphavirus replicons have been increasingly used as expression vectors for basic research, for the generation of vaccines, and for the production of recombinant proteins in industrial scale. The main approaches of laboratories in the recent years have been twofold. On one hand, they have discovered and characterized the enzymatic activities of the individual replicase proteins and on the other hand, they have studied the localization, membrane association, and other cell biological aspects of the replication complex.

Complete nucleotide sequence of the nonstructural protein genes of Semliki Forest virus

The nucleotide sequence coding for the nonstructural proteins of Semliki Forest virus has been determined from cDNA clones. The total length of this region is 7381 nucleotides, it contains an open reading frame starting at position 86 and ending at an UAA stop codon at position 7379-7381. This open reading frame codes for a 2431 amino acids long polyprotein, from which the individual nonstructural proteins are formed by proteolytic processing steps, so that nsPl is 537, nsP2 798, nsP3 482 and nsP4 614 amino acids. In the closely related Sindbis and Middelburg viruses there is an opal stop codon (UGA) between the genes for nsP3 and nsP4. Interestingly, no stop codon is found in frame in this region of the Semliki Forest virus 42S RNA. In other aspects the amino acid sequence homology between Sindbis, Middelburg and Semliki Forest virus nonstructural proteins is highly significant.

Detection of immunologically cross-reacting capsid protein of alphaviruses on the surfaces of infected L929 cells

Hyperimmune, but not normal immune, monospecific antiserum made to capsid protein of Sindbis virus (SIN) was found to cause cytolysis equally well of both SIN- and Semliki Forest virus-infected L929 cells in antibody-dependent, complement-mediated cytotoxicity assays. The cell surface reactivity of the hyperimmune antiserum was also demonstrated by solid-phase radioimmune assays with unfixed infected cells or infected cells fixed with low concentrations of glutaraldehyde (0.025%) before reactivity with antisera. Higher concentrations of glutaraldehyde lowered the sensitivity of detection. Purified SIN capsid protein specifically inhibited antibody-dependent, complement-mediated cytotoxicity by the monospecific anti-capsid protein serum on SIN- and Semliki Forest virus-infected target cells. That hyperimmune anti-SIN serum also cross-reacts with capsid protein on the surface of Semliki Forest virus-infected cells was suggested by the fact that capsid protein inhibited cross-cytolysis in the antibody-dependent, complement-mediated cytotoxicity assay. The latter antiserum was collected after repeated injections of purified virions over a 9-month period. The results suggest that hyperimmune monospecific antisera made to SIN capsid protein or hyperimmune antisera to SIN or Semliki Forest virions detect homologous and cross-reacting capsid protein determinants on the surface of infected cells.

Semliki Forest virus: a probe for membrane traffic in the animal cell

The traffic among the cellular compartments is thought to be mediated by membrane vesicles, which bud from one compartment and fuse with the next. Despite the continuous exchange of membrane components among them, the organelles maintain their characteristic protein and lipid compositions such that the traffic remains selective, thus, avoiding intermixing of components. This membrane traffic recycles components from the cell surface to the interior of the cell and back to the cell surface again. The membrane traffic between the ER and the cell surface involves a major sorting problem. Little is known of how the animal cell has solved this problem in molecular terms. One experimental tool in this direction is provided by some enveloped animal viruses, which mature at the cell surface of infected cells. Such viruses include influenza virus, Semliki Forest virus (SFV), Sindbis virus, and vesicular stomatitis virus (VSV). They are extremely simple in makeup and hence are very well characterized. The purpose of this article is to illustrate the use of the enveloped viruses as tools in the study of membrane traffic in the animal cell. This is done in the context of the life cycle of the virus in the host cell. The article will be concerned mainly with Semliki Forest virus (SFV), which is the virus that has been worked upon in the chapter. SFV belongs to the alphaviruses, a genus of the togavirus family.

Nonstructural proteins of Semliki Forest virus: synthesis, processing, and stability in infected cells

The synthesis of the nonstructural (ns) proteins of Semliki Forest virus was studied in vivo. The fourth ns protein, ns60, was identified and isolated. The order of translation (NH2-ns70-ns86-ns60-ns72-COOH) was determined by using various labeling procedures after or in the presence of a hypertonic block of translation initiation. A sequential labeling procedure was devised to specifically label defined segments of the polyprotein. The specific labeling procedures allowed isolation of the four ns proteins in radiochemically pure form by gradient polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The four ns proteins were shown to have different primary structures by digestion with V8 protease of Staphylococcus aureus. The processing of the ns polyprotein and the stability of the mature ns proteins were studied by pulse-chase experiments. The cleavage of each of the proteins from the polyprotein took place within 2 to 3 min after the translation of the polypeptide chain. The N-terminal protein, ns70, appeared in its mature form later than ns86, which follows it in the polyprotein, suggesting that ns70 undergoes a post-translational modification. The migration of the C-terminal protein, ns72, immediately after a pulse was slightly faster than after a chase, suggesting that ns72 also undergoes a post-translational modification other than a cleavage. The half-life of ns72 was shorter than that of the other ns proteins.

The 5'-terminal sequences of the genomic RNAs of several alphaviruses

The 5'-terminal sequences of the genomic RNAs of several alphaviruses have been determined. The nucleotide sequences at the extreme 5' termini are not highly conserved among the alphaviruses, but a similar stem and loop structure, which begins at the 5' end and utilizes about the first 40 nucleotides, can be formed in each case. Downstream from this structure, beginning about 150 nucleotides from the 5' end, a conserved sequence of 51 nucleotides is found which can form two stable hairpin structures. Examination of the 5'-terminal and 3'-terminal sequences suggests that part of this conserved nucleotide sequence may be involved in cyclization of the RNA. A model is proposed for the function of the 5'-terminal sequences in RNA replication. In addition, sequence homologies among these RNAs strongly support the hypothesis that an AUG codon, which occurs at 60 to 80 nucleotides from the 5' end, depending on the virus, and which may or may not be the first AUG codon, is used for initiation of translation of the non-structural proteins and allows a comparison of the deduced amino acid sequences in the NH2-terminal regions.

The core protein of alphaviruses. 1. Purification of peptides and complete amino-acid sequence of Semliki Forest virus core protein

The primary structure of the core protein of Semliki Forest virus has been established by protein chemical characterization of 102 peptides, generated by digestion with trypsin, pepsin, thermolysin, and by partial acid cleavage of the protein. Besides a difference in one position, the sequence as established by these experiments is in agreement with the sequence predicted from the nucleotide sequence of the mRNA [Garoff et al. (1980) Proc. Natl Acad. Sci. USA, 77, 6376-6380]. The core protein has a blocked N terminus, consists of 267 amino acid residues, and has the following amino acid composition: Asp12, Asn9, Thr16, Ser10, Glu11, Gln15, Pro23, Gly20, Ala23, Val19, Met8, Ile11, Leu9, Tyr7, Phe6, His7, Lys37, Arg15, Trp5, Cys4, and an Mr of 29919. It contains 22.1% basic amino acids, mainly lysines, compared with a total of 8.6% acidic residues. The resulting surplus of positive charge is located in the N-terminal half of the protein (predominantly arginines at positions 12-21 and lysines at positions 66-114). Other amino acids are also unevenly distributed; proline and glutamine are accumulated in the N-terminal half of the sequence whereas histidine, glycine and the acidic residues are mainly present in the C-terminal part. This distribution suggests that the virus core protein consists of two or more structural domains.

Nucleotide sequence at the junction between the nonstructural and the structural genes of the semliki forest virus genome

The nucleotide sequence at the junction between the nonstructural and the structural genes of the Semliki Forest virus 42S RNA genome has been determined from cloned cDNA. With the aid of S1-mapping, we have located the 5' end of the viral 26S RNA on this sequence. The 26S RNA is homologous to the 3' end of the 42S RNA and is used as a messenger for the structural proteins of the virus. The nucleotide sequence in the noncoding 5' region of the 26S RNA (51 bases) was thus established, completing the primary structure of the 26S RNA molecule (for earlier sequence work, see Garoff et al., Proc. Natl. Acad. Sci. U.S.A. 77:6376-6380, 1980, and Garoff et al., Nature (London) 288:236-241, 1980). An examination of the nucleotide sequences upstream from the initiator codon for the structural proteins on the 42S RNA genome shows that all reading frames are effectively blocked by stop codons, which means that the nonstructural genes in the 5' end of the 42S RNA molecule do not overlap with the structural ones at the 3' end of the molecule.

Intracellular murine hepatitis virus-specific RNAs contain common sequences

A major polyadenylated viral RNA of approximately 0.8 × 10⁶ daltons was isolated from murine hepatitis virus (A59)-infected cells by preparative polyacrylamide gel electrophoresis in formamide. This RNA was shown to encode the viral nucleocapsid protein by direct in vitro translation in a cell-free, reticulocyte-derived system. Single stranded ³²P-labeled complementary DNA was prepared from this RNA and was demonstrated to be virus specific. Using this complementary DNA in a Northern blotting procedure, we were able to identify six major virus-specific intracellular RNA species with estimated molecular weights of 0.8, 1.1, 1.4, 1.6, 3, and 4 × 10⁶ daltons. All of these RNA species were polyadenylated. Our results support the idea that coronavirus-infected cells contain multiple intracellular polyadenylated RNAs which share common sequences.

Synthesis and processing of Semliki Forest virus-specific nonstructural proteins in vivo and in vitro

A large short-lived virus-specific nonstructural protein with an apparent molecular weight of about 250000 (nsp250) has been isolated from cells infected with the temperature-sensitive mutants ts-4 and ts-6 of the Semliki Forest virus. nsp250 contained all peptides characteristic of the two previously identified nonstructural precursor proteins, nsp155 and nsp135, as revealed by limited proteolysis with Staphylococcus aureus V8 protease. Thus nsp250 is probably the translational product of the 5' two-thirds of the 42-S RNA genome which codes for the virus-specific nonstructural proteins. A second viral nonstructural precursor protein, nsp220, was also characterized by peptide mapping. This protein contained all the peptides of nsp155, and several but not all of the peptides of nsp135. Some peptides were demonstrated which possibly are derived from ns60, the only nonstructural protein not yet isolated. Small amounts of proteins with identical mobility to nsp250 and nsp220 were synthesized at 38 degrees C in micrococcal-nuclease-treated rabbit reticulocyte lysate in response to virion 42-S RNA from the ts-6 mutant. The product of the wild-type 42-S RNA in vitro contained, in addition to nsp220 and nsp155, polypeptides which comigrated with ns86, ns72 and ns70, indicating processing of the translational product. The authenticity of nsp220, nsp155 and ns70 synthesized in vitro was confirmed by limited proteolysis with V8 protease.

Nucleotide sequence of cdna coding for Semliki Forest virus membrane glycoproteins

The genes coding for the three membrane polypeptides of Semliki Forest virus have been sequenced and the primary structures of the proteins deduced. The amino acid sequence gives further insight into how the transmembrane structure of the three-chain virus membrane glycoprotein is generated in the infected cell.

The capsid protein of Semliki Forest virus has clusters of basic amino acids and prolines in its amino-terminal region

The amino acid sequence of the capsid (C) protein was deduced from the nucleotide sequence of the C gene. This part of the viral 42S RNA genome was transcribed into double-stranded cDNA. The cDNA was cloned in the Escherichia coli chi 1776-pBR322 host-vector system and then the base sequence was determined with the technique described by Maxam and Gilbert. The amino acid sequence of the C protein shows a clustering of basic amino acids and prolines within the first 110 amino acids.

Analysis of Semliki-Forest-virus structural proteins to illustrate polyprotein processing of alpha viruses

The four structural proteins of Semliki Forest virus were purified in an amount of 30-50 nmol by preparative sodium dodecylsulfate/polyacrylamide gel electrophoresis. Each protein was subjected to N-terminal structural analysis by degradation in a liquid-phase sequencer. About 20 residues were determined for each of the two membrane glycoproteins E1 and E2. The amino acid sequence of E1 but not that of E2 showed extensive homology to the corresponding proteins of the closely related Sindbis virus. Both E1 and E2 seem to lack a signal sequence at the N terminus, since the proportion of polar amino acids in this region deviates from the proportion in the known hydrophobic signal sequences. The envelope glycoprotein E3 and the capsid protein did not yield any significant result on Edman degradation, suggesting that they have blocked N-terminal amino groups.

Post-Translational Proteolytic Cleavage of In Vitro-Synthesized Turnip Yellow Mosaic Virus RNA-Coded High-Molecular-Weight Proteins

In a reticulocyte lysate, turnip yellow mosaic virus genomic RNA directs the synthesis of two proteins with molecular weights of 150,000 (150K) and 195K. We present evidence that the larger protein is processed in vitro, after its completion, in at least three fragments. The NH 2 -terminal fragment (82K) and the COOH-terminal fragment (78K) have been well characterized by different methods. The fact that the 150K protein is not cleaved in vitro, although it contains the regions that are processed in the 195K protein, could be of fundamental biological significance for the expression of the viral genes: a single polypeptide chain could be processed in several ways, leading to different peptides with distinct biological activities.

The nucleotide sequences of the 5'-terminal T1 oligonucleotides of Semliki-Forest-virus 42-S and 26-S RNAs are different

To study the mechanism of the synthesis of Semliki Forest virus (SFV) 26-S RNA, we have isolated the 5'-terminal 'cap'-containing RNase-T1-resistant oligonucleotide (T1 cap) from the genomic 42-S RNA and from the subgenomic 26-S RNA and determined their nucleotide sequences. The T1 caps were purified from 32P-labelled RNAs on two successive two-dimensional fractionation systems: (a) electrophoresis on cellulose acetate paper followed by homochromatography and (b) two-dimensional polyacrylamide gel electrophoresis. The T1 caps derived from the two RNAs had different mobilities in both systems. Their nucleotide sequence was found to be: m7G(5')ppp-(5')ApUpGp- for the 42-S RNA and m7G(5')ppp(5')ApUpUpGp- for the 26-S RNA, respectively. Thus, it appears that the 26-S RNA is not formed by initiation of the RNA polymerase at the 3' end of the negative-strand template followed by 'cleavage and splicing' or as the result of a 'polymerase jump'. Our results, instead, favour the model of internal initiation of the polymerase on the 42-S negative-strand RNA template.

Initiation and processing in vitro of the primary translation products of guinea-pig caseins

1. Guinea-pig caseins synthesized in a mRNA-directed wheat-germ cell-free protein-synthesizing system represent the primary translation products, even though they appear to be of lower molecular weight when analysed by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis in parallel with caseins isolated from guinea-pig milk. 2. Identification of the N-terminal dipeptide of the primary translational product of caseins A, B and C and alpha-lactalbumin showed that all shared a common sequence, which was identified as either Met-Arg or Met-Lys. 3. Procedures utilizing methionyl-tRNAfMet or methionyl-tRNAMet in the presence or absence of microsomal membranes during translation provide a rapid method of distinguishing between N-terminal processing of peptides synthesized in vitro and other post-translational modifications (glycosylation, phosphorylation), which also result in a change in mobility of peptides when analysed by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. 4. The results demonstrate that guinea-pig caseins, in common with most other secretory proteins, are synthesized with transient N-terminal 'signal'-peptide extensions, which are cleaved during synthesis in the presence of microsomal membranes.

Functional defects of RNA-negative temperature-sensitive mutants of Sindbis and Semliki Forest viruses

Defects in RNA and protein synthesis of seven Sindbis virus and seven Semliki Forest virus RNA-negative, temperature-sensitive mutants were studied after shift to the restrictive temperature (39 degrees C) in the middle of the growth cycle. Only one of the mutants, Ts-6 of Sindbis virus, a representative of complementation group F, was clearly unable to continue RNA synthesis at 39 degrees C, apparently due to temperature-sensitive polymerase. The defect was reversible and affected the synthesis of both 42S and 26S RNA equally, suggesting that the same polymerase component(s) is required for the synthesis of both RNA species. One of the three Sindbis virus mutants of complementation group A, Ts-4, and one RNA +/- mutant of Semliki Forest virus, ts-10, showed a polymerase defect even at the permissive temperature. Seven of the 14 RNA-negative mutants showed a preferential reduction in 26S RNA synthesis. The 26S RNA-defective mutants of Sindbis virus were from two different complementation groups, A and G, indicating that functions of two viral nonstructural proteins ("A" and "G") are required in the regulation of the synthesis of 26S RNA. Since the synthesis of 42S RNA continued, these functions of proteins A and G are not needed for the polymerization of RNA late in infection. The RNA-negative phenotype of 26S RNA-deficient mutants implies that proteins regulating the synthesis of this subgenomic RNA must have another function vital for RNA synthesis early in infection or in the assembly of functional polymerase. Several of the mutants having a specific defect in the synthesis of 26S RNA showed an accumulation of a large nonstructural precursor protein with a molecular weight of about 200,000. One even larger protein was demonstrated in both Semliki Forest virus- and Sindbis virus-infected cells which probably represents the entire nonstructural polyprotein.

Ribosome-protected fragments from sindbis 42-S and 26-S RNAs

Sindbis virus 42-S and 26-S RNAs labeled with 32P were purified from infected chick embryo fibroblasts. The RNA's were incubated in the presence of a wheat germ cell-free translating system under conditions that yielded 40-S and 80-S initiation complexes. After digestion with RNase A, ribosome-protected fragments were isolated by polyacrylamide gel electrophoresis and compared with respect to number, size, cap content and oligonucleotide composition. The two RNA species yielded several fragments of chain length about 35--40 nucleotides from 80S complexes and up to 60--65 nucleotides from 40-S complexes. The 5'-terminal capped sequence, m7 GpppA-U-G that is present in both Sindbis virus RNA's, was not retained in any of the ribosome-protected fragments. Fingerprint analyses indicated that the fragments derived from 40S and 80-S initiation complexes of each species of RNA were overlapping, but the fragments from 42-S and 26-S RNAs were unrelated. The complexity of the fingerprints were consistent with protection of a single, different initiation site in each Sindbis virus RNA.

Anatomy of the RNA and gene products of MC29 and MH2, two defective avian tumor viruses causing acute leukemia and carcinoma: evidence for a new class of transforming genes

The RNA species of the defective avian acute leukemia virus MC29 and of the defective avian carcinoma virus MH2 and of their helper viruses were analyzed using gel electrophoresis, fingerprinting of RNase T1-resistant oligonucleotides, RNA-cDNA hybridization and in vitro translation. A28S RNA species, of 5700 nucleotides, was identified as MC29- or MH2-specific. MC29 RNA shared 4 out of about 17 and MH2 RNA at least 1 out of 16 T1-oligonucleotides with several other avain tumor virus RNAs. In addition MC29 and MH2 RNAs shared 2 oligonucleotides which were not found in any other viral RNA tested. 60% of each 28S RNA could be hybridized by DNA complementary to other avian tumor virus RNAs (group-specific) but 40% could only be hybridized by homologous cDNA (specific). Src gene-related sequences of Rous sarcoma virus were not found in MC29 or MH2 RNA. The specific and group-specific sequences of MC29, defined in terms of their T1-oligonucleotides, were located on a map of all T1-oligonucleotides of viral RNA. Specific sequences mapped between 0,4 and 0,7 map units from the 3'poly(A) end and group-specific sequences mapped between 0 and 0,4 and 0,7 and 1 map units. The MC29-specific RNA segment was represented by 6 oligonucleotides, two of which were those shared only by MC29 and MH2 RNAs. In vitro translation of MC29 RNA generated a major 120 000 dalton protein and minor 56 000 and 37 000 dalton proteins. The 120 000 dalton protein shared sequences with the proteins of the avian tumor viral gag gene, which maps at the 5' end of independently replicating viruses. Since a gag gene-related oligonucleotide was also found near the 5' end of MC29 RNA, we propose that the 120 000 MC29 protein was translated from the 5' 60% of MC29 RNA. It would then include sequences of the defective gag gene as well as MC29-specific sequences. Since both MC29 and MH2 lack the src (sarcoma) gene of Rous sarcoma virusk it is concluded that they contain a distinct class of transforming (onc) genes. We propose that the specific sequences of MC29 and MH2 represent all, or part of, their onc genes because the onc genes of MC29 and MH2 are specific and represent the only known genetic function of these viruses. If this proposal is correct, the onc genes of MC29 and MH2 would be related, because the specific RNA sequence of MC29 shares 2 of 6 oligonucleotides with MH2. It would also follow that the 120 000 dalton MC29 protein is a probable onc gene product, because it is translated from MC29-specific (and group-specific) sequences and because both MC29- and MH2-transformed cells contain specific 120 000 and 100 000 dalton proteins, respectively.

Characterization of the amino-terminal tryptic peptide of simian virus 40 small-t and large-T antigens

Simian virus 40 small-t and large-T antigen were synthesized in vitro and labeled with methionine donated by initiator tRNA. Tryptic peptide fingerprinting was used to identify the amino-terminal peptide of the two proteins. Similar fingerprint analysis of small-t and large-T made in vitro in the absence of acetyl coenzyme A showed that the mobility of the amino-terminal peptide was changed under these conditions and suggested that it is acetylated. These data establish that the amino-terminal methionine residue of simian virus 40 small-t and large-T results from an initiation event, not post-translational cleavage, and provides additional evidence that the amino terminus of both proteins is acetylated. The identification of the amino-terminal peptide provides a useful marker for further studies on different forms of T-antigen from cells infected with and transformed by simian virus 40 and related viruses.

Specific RNA sequences and gene products of MC29 avian acute leukemia virus

The 28S RNA of the defective avian acute leukemia virus MC29 contains two sets of sequences: 60% are hybridized by DNA complementary to other avian tumor virus RNAs (group-specific cDNA) and 40% are hybridized only by MC29-specific cDNA. Specific and group-specific sequences of viral RNA, defined in terms of their large RNase T(1)-resistant oligonucleotides, were located on a map of all large T(1) oligonucleotides of viral RNA. Oligonucleotides representing MC29-specific sequences of viral RNA mapped between 0.4 and 0.7 unit from the 3'-poly(A) end. Oligonucleotides of group-specific sequences mapped between 0 and 0.4 and between 0.7 and 1 map unit. Cell-free translation of viral RNA yielded three proteins with approximate molecular weights of 120,000, 56,000, and 37,000, termed P120(mc), P56(mc), and P37(mc). P120(mc) contained both MC29-specific peptides and serological determinants and peptides of the conserved, internal group-specific antigens of avian tumor viruses. P120(mc) is translated only from full-length 28S RNA. Furthermore, MC29 RNA contains sequences related to the group-specific antigen gene (gag), near the 5' end, which are followed by MC29-specific sequences. We conclude that this protein is translated from the 5' 60% of the RNA, and that it includes a segment translated from the specific sequences. It is suggested that the transforming (onc) gene of MC29 may consists of the specific and some group-specific RNA sequences and that P120(mc), which is also found in transformed cells, may be the onc gene product.

Polyoma virus has three late mRNA's: one for each virion protein

Polyoma virus mRNA, isolated from the cytoplasm of 3T6 cells late after infection and purified by hybridization to HpaII fragment 3 of polyoma virus DNA, was separated on 50% formamide-containing sucrose density gradients, and the fractionated RNA was recovered and translated in vitro. Analysis of the cell-free products showed that the minor virion protein VP3 was synthesized from an mRNA sedimenting at approximately 18S betweeen the 19S VP2 mRN and the 16S VP1 mRNA. Other experiments showed that the VP2 and VP3 can be labeled with formyl methionine from initiator tRNA. We conclude that there are three late polyoma virus mRNA's, each directing the synthesis of only one viral capsid protein.

Togavirus RNA: reversible effect of urea on genomes and absence of subgenomic viral RNA in Kunjin virus-infected cells

Electrophoretic analyses showed that no RNase-sensitive RNA smaller than the genome was specified by the flavivirus Kunjin in infected Vero cells during the period of maximum RNA and protein synthesis. In contrast, RNA extracted from Sindbis virus-infected cells under similar conditions included the expected 42S RNA (equivalent to the genome) and the smaller 26S (interjacent) RNA. Treatment of the genome of both togaviruses with 12 M urea produced a reversible (possibly conformational) change; measurement of the molecular weights of the treated RNAs by co-electrophoresis with fully denatured ribosomal RNA markers in SDS-polyacrylamide gels yielded a value of 2.1 X 10(6) if 8 M urea was incorporated in the gels and 4.2 X 10(6) if urea was omitted from the gels. These results indicate that flavivirus messenger RNA is represented solely by the intact genome of m.wt. 4.2 X 10(6).

Synthesis of Sindbis virus nonstructural polypeptides in chicken embryo fibroblasts

The identification of eight previously undescribed polypeptides in chicken embryo cells infected with Sindbis virus is reported. Seven of these polypeptides were distinguishable from the virus structural polypeptides and their precursors by their molecular weights and tryptic peptide maps. The eighth was closely related to pE2 (Schlesinger and Schlesinger, 1973), a precursor to one of the virus particle glycoproteins. Pulse-chase experiments and the use of an inhibitor of proteolytic cleavage allowed a division of the seven nonstructural (NS) polypeptides into three stable end products (NS p89, NS p82, and NS p60) and four precursors (p230, p215, p150, and p76). The labeling kinetics after synchronous initiation of translation indicated that synthesis of the NS polypeptides started at a single site and showed that the order of the genes coding for the NS polypeptides was (5' leads to 3') NS p60, NS p89, and NS p82. Short-pulse experiments under conditions of both synchronized and nonsynchronized translation suggested that cleavage of the primary translation product of the NS genes occurred only after its synthesis was completed and that the first cleavage removed the C-terminal polypeptide. From these and other experiments, we propose a detailed scheme for the synthesis and processing of Sindbis virus NS polypeptides.

Control of protein synthesis in Semliki forest virus-infected cells

Protein synthesis in Semliki forest virus-infected chicken embryo cells was studied by labeling them with [35S]methionine for short periods at different times after infection, with or without synchronization of protein synthesis by the hypertonic block technique. The rate of host-cell protein synthesis declined almost linearly in inverse correlation to the increase in the amount of virus specific RNA. At 5.5 h postinfection, the host-cell protein synthesis was reduced by about 70%. The viral structural proteins were detectable with certainty at 3.5 h postinfection, and their rate of synthesis increased linearly parallel to the amount of their messenger, the 26S RNA. This suggests that the rate of synthesis of the structural proteins is controlled at the level of transcription. The rate of synthesis of the virus-specific nonstructural proteins attained its maximum between 3 and 4 h postinfection and declined thereafter, wheras the amount of their messenger, the 42S RNA, continued to increase linearly in the cells. Thus, the messenger activity of the 42S RNA is reduced in the late phase of infection compared with its activity in the early phase.

Rabies virus protein synthesis in infected BHK-21 cells

Rabies virus specific polypeptide synthesis was examined under hypertonic conditions, which selectively inhibit cellular protein synthesis. The rabies virus proteins (L, G, N, M1, M2) were synthesized throughout the course of infection, with little change in their relative rates of synthesis. The rates of synthesis of the G and M1 polypeptides were more sensitive to increasing osmolarity than those of the L, N, and M2 polypeptides. Extrapolation to isotonicity of the results obtained under hypertonic conditions indicated that the molar ratios of the polypeptides synthesized under normal conditions were 0.4 (L), 64 (G), 100 (N), 75 (M1) and 35 (M2). A high-molecular-weight polypeptide (190,000), designated polypeptide L, was repeatedly detected both in infected cells and in extracellular virus. The estimated number of L polypeptide molecules per virion was 33. The synthesis of a viral glycoprotein precursor, designated gp78, , preceded the appearance of the mature viral glycoprotein in infected cells labeled with [3H]glucosamine under isotonic conditions. In cells labeled under hypertonic conditions, little or no mature viral glycoprotein was detected, but a virus-specific glycoprotein with an electrophoretic mobility similar to that of gp78 was observed. This glycoprotein could be chased into mature viral glycoprotein when the hypertonic conditions were made isotonic. These results suggest that a reversible block of viral glycoprotein synthesis occurs under hypertonic conditions.