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

Regulation of the sequential processing of Semliki Forest virus replicase polyprotein

The replication of most positive-strand RNA viruses and retroviruses is regulated by proteolytic processing. Alphavirus replicase proteins are synthesized as a polyprotein, called P1234, which is cleaved into nsP1, nsP2, nsP3, and nsP4 by the carboxyl-terminal protease domain of nsP2. The cleavage intermediate P123+nsP4 synthesizes minus-strand copies of the viral RNA genome, whereas the completely processed complex is required for plus-strand synthesis. To understand the mechanisms responsible for this sequential proteolysis, we analyzed in vitro translated Semliki Forest virus polyproteins containing noncleavable processing sites or various deletions. Processing of each of the three sites in vitro required a different type of activity. Site 3/4 was cleaved in trans by nsP2, its carboxyl-terminal fragment Pro39, and by all polyprotein proteases. Site 1/2 was cleaved in cis with a half-life of about 20-30 min. Site 2/3 was cleaved rapidly in trans but only after release of nsP1 from the polyprotein exposing an "activator" sequence present in the amino terminus of nsP2. Deletion of amino-terminal amino acids of nsP2 or addition of extra amino acid residues to its amino terminus specifically inhibited the protease activity that processes the 2/3 site. This sequence of delayed processing of P1234 would explain the accumulation of P123 plus nsP4, the early short-lived minus-strand replicase. The polyprotein stage would allow correct assembly and membrane association of the RNA-polymerase complex. Late in infection free nsP2 would cleave at site 2/3 yielding P12 and P34, the products of which, nsP1-4, are distributed to the plasma membrane, nucleus, cytoplasmic aggregates, and proteasomes, respectively.

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.

Proteolytic processing of Semliki Forest virus-specific non-structural polyprotein by nsP2 protease

The RNA replicase proteins of Semliki Forest virus (SFV) are translated as a P1234 polyprotein precursor that contains two putative autoproteases. Point mutations introduced into the predicted active sites of both proteases nsP2 (P2) and nsP4 (P4), separately or in combination, completely abolished virus replication in mammalian cells. The effects of these mutations on polyprotein processing were studied by in vitro translation and by expression of wild-type polyproteins P1234, P123, P23, P34 and their mutated counterparts in insect cells using recombinant baculoviruses. A mutation in the catalytic site of the P2 protease, C(478)A, (P2(CA)) completely abolished the processing of P12(CA)34, P12(CA)3 and P2(CA)3. Co-expression of P23 and P12(CA)34 in insect cells resulted in in trans cleavages at the P2/3 and P3/4 sites. Co-expression of P23 and P34 resulted in cleavage at the P3/4 site. In contrast, a construct with a mutation in the active site of the putative P4 protease, D(6)A, (P1234(DA)) was processed like the wild-type protein. P34 or its truncated forms were not processed when expressed alone. In insect cells, P4 was rapidly destroyed unless an inhibitor of proteosomal degradation was used. It is concluded that P2 is the only protease needed for the processing of SFV polyprotein P1234. Analysis of the cleavage products revealed that P23 or P2 could not cleave the P1/2 site in trans.

The Semliki-Forest-virus-specific nonstructural protein nsP4 is an autoproteinase

The Semliki-Forest-virus-specific nonstructural proteins are translated as a large polyprotein (2431 amino acid residues), from which the mature polymerase components nsP1, nsP2, and nsP4 are released by proteolytic cleavages. The complete ns polyprotein (P1234) can be cleaved in two alternative ways yielding either P123 (with sequences of nsP1, nsP2 and nsP3) and nsP4 or P12 (nsP1 plus nsP2) and P34 (nsP3 plus nsP4). We studied the possible autoproteolytic role of nsP4 involved in the cleavage between nsP3 and nsP4 in an in vitro transcription-translation system. cDNAs encoding P34 precursor and shorter precursor protein segments covering the nsP3-nsP4 cleavage region, were cloned under the T7 RNA polymerase promoter. The mRNAs synthesized in vitro were capped and translated in rabbit reticulocyte lysates. The translational products were analyzed by SDS/PAGE. The precursor proteins containing nsP4 sequences were cleaved yielding the products with expected sizes, indicating that the cleavage took place at the nsP3-nsP4 junction. By deleting and truncating the cDNA coding for nsP4, the proteolytic activity was mapped within the 102 amino-terminal amino acids of nsP4. The cleavage between nsP3 and nsP4 can be inhibited by pepstatin A and probably takes place in cis, since exogenously added nsP4 was unable to mediate it.

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 genomic-length soybean mosaic virus RNA on polyribosomes of infected soybean leaves

Soybean mosaic virus (SMV)-related RNAs were examined in both polyribosomal and nonpolyribosomal fractions of systemically infected soybean leaves. Viral RNAs were detected by Northern blot hybridization analysis using two cloned SMV-cDNAs representing different regions of the viral genome as hybridization probes. Genomic length SMV-RNA (Mr of 3.3 X 10(6] was found in specific association with EDTA-sensitive polyribosomes of infected leaves, indicating that it functions as a messenger RNA in these cells. A smaller SMV-related RNA (Mr of 1.6 X 10(6] was sometimes detected in the polyribosomal fraction; however, reconstruction experiments indicate that this RNA is a breakdown product of the genomic-length RNA, generated during cell fractionation or RNA extraction. Two other SMV-related RNAs with Mr of 2.0 and 0.78 X 10(6) were sometimes detected in infected cells and were not generated from genomic SMV-RNA or intact virus particles in reconstruction experiments. However, these RNAs were exclusively associated with the EDTA-resistant, nonpolyribosomal fraction of infected cells. These data suggest that genomic-length SMV-RNA is the only viral RNA which is translated in these infected plants.

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.

Reduced synthesis of Sindbis virus negative strand RNA in cultures treated with host transcription inhibitors

Host cell involvement in Sindbis virus (SB) RNA synthesis was examined in cells which had been treated before infection with actinomycin D or alpha-amanitin (alpha-A). Overall synthesis of SB RNA was reduced significantly in CHO cells treated for 18 h before infection with alpha-A. However, SB RNA was produced at near normal levels in CHOama-1 cells, a line which contains an alpha-A-resistant RNA polymerase II. In BHK or CHO cells infected with SBamr, a mutant which replicates normally in cells pretreated with either actinomycin D or alpha-A, viral RNA synthesis was not decreased. The levels of negative strand RNA and of replicative forms I, II, and III in SB-infected cells were progressively reduced with increasing times of pretreatment with host transcription inhibitors, indicating fewer functional replicative intermediates in treated cells. Replicative events after replicative intermediate formation also were inhibited but only to the extent predicted by the reduction in replicative intermediates. Similarly, events preceding negative strand synthesis, adsorption, penetration, uncoating, and translation of nonstructural proteins, apparently were not impeded in treated cells. Therefore, our results are consistent with the involvement of a host component after translation of the nonstructural proteins but before or during the synthesis of SB negative strand RNA.

Proteolytic maturation of the turnip-yellow-mosaic-virus polyprotein coded in vitro occurs by internal catalysis

The genomic RNA of turnip yellow mosaic virus is translated in vitro into two major high-molecular-weight proteins, the larger of which (Mr 195 000) undergoes post-translational cleavage. The mechanism of formation of the primary cleavage products (Mr 120 000 and Mr 78 000) of the 195 000-Mr protein has been examined. The fact that cleavage partly occurs at a rate insensitive to dilution of the 195 000-Mr protein is suggestive of an intramolecular mechanism of proteolytic maturation.

18S defective interfering RNA of Semliki Forest virus contains a triplicated linear repeat

The nucleotide sequence of a nearly full-length cloned cDNA copy of an 18S defective interfering (DI) RNA of Semliki Forest virus has been determined. This corresponded to a major virus-specific cytoplasmic RNA species at the 11th undiluted passage of the virus in BHK cells. The 1652-nucleotide-long sequence consists of a unique 5'-terminal sequence followed by three tandem 484-nucleotide repeat units derived from the 5' two-thirds of the viral genome and a unique sequence of 106 nucleotides preceding the poly(A) of the 3' terminus. One of the tandem 484-nucleotide repeat units contains an extra segment of 60 nucleotides. Hybridization experiments showed that the cloned cDNA was colinear with an 18S DI RNA and that it contained an approximately 320-nucleotide-long segment colinear with the viral genomic RNA. Analysis of 18S DI RNA oligonucleotide fingerprints revealed that the molecule studied and the heterogeneous DI RNA population contain similar repeated sequences. The mechanism by which the DI RNAs are generated is not known, but it seems likely that multiple internal deletions and duplications are involved.

Cell-free synthesis and glycosylation of the major human-red-cell sialoglycoprotein, glycophorin A

The human erythroid cell line, K562, synthesizes the major red cell sialoglycoprotein, glycophorin A. We have isolated an mRNA fraction which codes for glycophorin A from K562 cells and studied the synthesis of the sialoglycoprotein in a rabbit reticulocyte cell-free system. In the absence of membranes a precursor form of glycophorin A was synthesized. This was identified using specific anti-(glycophorin A) serum. The apparent molecular weight of the carbohydrate-free precursor of glycophorin A was 19 500. This exceeds the molecular weight of the glycophorin A apoprotein by approximately 5000. In the presence of membranes from dog pancreas, the synthesized glycophorin A precursor was N-glycosylated and probably also O-glycosylated. The oligosaccharide chains remained incomplete and the glycoprotein synthesized in vitro corresponded to the glycosylated precursor of glycophorin A obtained in intact cells.