Characterization of the mRNA's for the polyoma virus capsid proteins VP1, VP2, and VP3

Cytomegalovirus assembly protein nested gene family: four 3'-coterminal transcripts encode four in-frame, overlapping proteins

The genomic region encoding the assembly protein of simian cytomegalovirus (CMV) strain Colburn has been cloned, sequenced, and found to be organized as a nested set of four in-frame, 3'-coterminal genes, each with its own TATA promoter element and translational start codon, and all using a single 3' polyadenylation signal. The 3' end of the longest open reading frame (1.770 bp) was identical to the 930-bp sequence coding for the assembly protein precursor, as determined from a cDNA clone. The assembly protein coding region of human CMV strain AD169 was similarly organized, suggesting that both viral genomes could give rise to four independently transcribed 3'-coterminal RNAs coding for four overlapping, in-frame, carboxy-coterminal proteins. These predictions were tested and confirmed. Four mRNAs corresponding in size and sequence to those predicted were identified in both human and simian CMV-infected cells by using transcript-specific antisense oligonucleotide probes in Northern (RNA blot) assays. The 5' ends of the three largest of these Colburn transcripts were determined by S1 nuclease protection assays and found to map between the anticipated TATA sequences and corresponding translational start codons. The four predicted overlapping proteins were identified by immunoassays in lysates of simian and human CMV-infected cells by using an antiserum specific for the carboxyl end of the assembly protein precursor. The structural relationship of both sets of proteins was verified by comparing their peptide patterns following protein cleavage at tryptophan residues by N-chlorosuccinimide. The similar organization of the homologous coding regions in other herpesviruses into at least two nested, in-frame, 3'-coterminal genes is discussed.

Both VP2 and VP3 are synthesized from each of the alternative spliced late 19S RNA species of simian virus 40

The late 19S RNAs of simian virus 40 consist of a family of alternatively spliced RNAs, each of which contains open reading frames corresponding to all three of the virion proteins. Two approaches were used to test the hypothesis that each alternatively spliced 19S RNA species is translated to synthesize preferentially only one of the virion proteins. First, we analyzed the synthesis of virion proteins in simian virus 40 mutant-infected monkey cells that accumulate predominantly either only one spliced 19S RNA species or only the 19S RNAs. Second, we determined the virion proteins synthesized in a rabbit reticulocyte lysate programmed with specific, in vitro-transcribed 19S RNA species. These results indicated that VP2 and VP3, but not VP1, are synthesized from all 19S RNA species. Quantitative analysis of these data indicated that individual 19S RNA species containing a translation initiation signal upstream of the VP2 AUG codon were translated in a cell extract three- to fivefold less efficiently than were 19S RNA species lacking this signal and that the precise rate of synthesis of VP2 relative to VP3 varied somewhat with the sequence of the leader region. These data are consistent with the synthesis of VP2 and VP3 occurring by a leaky scanning mechanism in which initiation of translation at a specific AUG codon is affected by both (i) the intrinsic efficiency of ribosomes recognizing the sequences surrounding the AUG codon as an initiation signal and (ii) partial interference from 5'-proximal initiation signals and their corresponding open reading frames.

Myristic acid is coupled to a structural protein of polyoma virus and SV40

In the lytic cycle of papova viruses, both uncoating of the viral genome after infection and assembly of functional virions take place in the cell nucleus. The mechanisms by which newly internalized virions are targeted to the nucleus and viral DNA encapsidated into particles are poorly understood. Although the major capsid protein VP1 is involved in endocytosis, and largely defines virion structure, the functions of the minor proteins VP2 and VP3 have remained obscure. Here we show that VP2 from both polyoma virus and simian virus 40 (SV40) is covalently linked to myristic acid; this is the first report of a myristylated protein in the nucleus and of a fatty acid being important in the structure of a nonenveloped virus. We consider the implications of this unusual modification on encapsidation and suggest that VP2 may be a scaffolding protein for virion assembly.

The carboxyl 35 amino acids of SV40 Vp3 are essential for its nuclear accumulation

To identify the moiety responsible for nuclear localization of the SV40 structural protein Vp3 in its natural environment, a transfection vector containing the entire coding regions of Vp2, Vp3, and agnoprotein, and one-third of the coding region of Vp1, was constructed. Several mutations were introduced into the plasmid and the subcellular distribution of Vp3 or mutant Vp3 was examined following DEAE-dextran-mediated DNA transfection into TC7 cells. Our study shows that Vp3 is synthesized and is transported into the nucleus in the absence of Vp2, agnoprotein, and intact Vp1. However, in the absence of its carboxyl-terminal 35 amino acids, the truncated Vp3 is limited to a cytoplasmic and perinuclear accumulation. Thus, the carboxyl 35 amino acids of Vp3 are required for its nuclear localization and may contain a nuclear accumulation signal.

Primate cytomegalovirus glycoproteins: lectin-binding properties and sensitivities to glycosidases

The lectin-binding properties and glycosidase sensitivities of the virion glycoproteins of primate cytomegaloviruses (CMVs) were examined. Three simian CMV (SCMV) strains, including Colburn, and four human CMV (HCMV) strains were compared. Their proteins were separated in denaturing polyacrylamide gels and electrotransferred onto nitrocellulose, and the glycosylated species were visualized with iodinated concanavalin A or wheat germ agglutinin (WGA). Virions of both HCMV and SCMV strains contained six principal and several minor lectin-reactive bands. Neuraminidase treatment abolished WGA binding and reduced the charge and charge heterogeneity of the SCMV (i.e., Colburn) virion glycoproteins and had a similar, although less dramatic, effect on those of HCMV. The specificities of concanavalin A and WGA in these assays were evaluated with endo-beta-N-acetylglucosaminidase H and endo-beta-N-acetylglucosaminidase F, and a combination of lectins and glycosidases was used to demonstrate that many of the primate CMV glycoproteins contain both high-mannose and complex, N-linked oligosaccharides. Results suggest that the HCMV virion glycoproteins are more extensively glycosylated or have more completely processed carbohydrate side chains, or both, than their SCMV counterparts.

Characterization of phosphoproteins and protein kinase activity of virions, noninfectious enveloped particles, and dense bodies of human cytomegalovirus

Phosphorylation of the proteins of human cytomegalovirus (CMV) virions, noninfectious enveloped particles (NIEPs), and dense bodies was investigated. Analyses of particles phosphorylated in vivo showed the following. Virions contain three predominant phosphoproteins (i.e., basic phosphoprotein and upper and lower matrix proteins) and at least nine minor phosphorylated species. NIEPs contain all of these and one additional major species, the assembly protein. Dense bodies contain only one (i.e., lower matrix) of the predominant and four of the minor virion phosphoproteins. Two-dimensional (charge-size) separations in denaturing polyacrylamide gels showed that the relative net charges of the predominant phosphorylated species ranged from the basic phosphoprotein to the more neutral upper matrix protein. In vitro assays showed that purified virions of human CMV have an associated protein kinase activity. The activity was detected only after disrupting the envelope; it had a pH optimum of approximately 9 to 9.5 and required a divalent cation, preferring magnesium to manganese. In vitro, this activity catalyzed phosphorylation of the virion proteins observed to be phosphorylated in vivo. Peptide comparisons indicated that the sites phosphorylated in vitro are a subset of those phosphorylated in vivo, underscoring the probable biological relevance of the kinase activity. Casein, phosvitin, and to a minor extent lysine-rich histones served as exogenous phosphate acceptors. Arginine-rich and lysine-rich histones and protamine sulfate, as well as the polyamines spermine and spermidine, stimulated incorporation of phosphate into the endogenous viral proteins. Virions of all human and simian CMV strains tested showed this activity. Analyses of other virus particles, including three intracellular capsid forms (i.e., A, B, and C capsids), NIEPs, and dense bodies, indicated that the active enzyme was not present in the capsid. Rate-velocity sedimentation of disrupted virions separated the protein kinase activity into two fractions: one that phosphorylated exogenous casein and another that phosphorylated primarily the endogenous virion proteins.

Isolation of human cytomegalovirus intranuclear capsids, characterization of their protein constituents, and demonstration that the B-capsid assembly protein is also abundant in noninfectious enveloped particles

Two types of intranuclear capsids have been recovered from human cytomegalovirus (HCMV, strain AD169)-infected cells. By analogy with strain Colburn (simian CMV) particles, these have been designated as A- and B-capsids. Both types of capsids are composed of proteins with molecular weights of 153,000 (major capsid protein), 34,000 (minor capsid protein), 28,000, and 11,000 (smallest capsid protein). In addition to these species, B-capsids contain a 36,000-molecular-weight (36K) protein which has been designated as the HCMV "assembly protein," based on its similarities to counterparts in strain Colburn CMV (i.e., 37K protein) and herpes simplex virus (i.e., VP22a/p40/NC-3/ICP35e). Peptide comparisons established that the assembly protein of HCMV B-capsids and the 36K protein that distinguishes HCMV noninfectious enveloped particles from virions are the same, providing direct evidence that noninfectious enveloped particles are enveloped B-capsids.

Comparison of nonphosphorylated and phosphorylated species of polyomavirus major capsid protein VP1 and identification of the major phosphorylation region

The major virion protein of polyomavirus, VP1, consists of about six isoelectric species designated A through F. The minor species D, E, and F are phosphorylated and are thought to serve as viral receptors. We first wanted to distinguish whether all VP1 species are derived by post-translational modification from a common amino acid sequence or whether one or more of the species contain a region(s) of altered amino acid sequence resulting from alternate mRNA processing. We compared the VP1 species by detailed peptide mapping with several combinations of specific protease and radioisotopic labels. This approach enabled us to examine more than 80% of the predicted VP1 sequence, including the amino-and carboxy-termini. We found no evidence of sequence differences among any of the VP1 species. The specific incorporation of 32Pi was found to be the same for all of the phosphorylated species. Comparison of the phosphorylation sites of in vivo 32Pi-labeled D, E, and F by peptide mapping showed them to be identical. Each phosphorylated species contained a single major phosphopeptide and several minor phosphopeptides. The major phosphoamino acid, identified by acid hydrolysis, was phosphothreonine, with phosphoserine also present. By using chemical cleavage methods, we localized the major phosphorylation region to a central portion of the VP1 sequence. We discuss some features of this region and relate this information to functional implications of phosphorylation.

Phosphorylation, maturational processing, and relatedness of strain Colburn matrix proteins

The intracellular 66,000 D (66K) and 69,000 D (69K) matrix-like phosphoproteins of strain Colburn cytomegalovirus (CMV) have been compared with each other and with their electrophoretic counterparts in the virion. Three lines of evidence indicate that the 66K and 69K proteins are products of separate genes, and that the intracellular and virion species are closely related. First, "pulse-chase" radiolabeling experiments showed that these proteins have separate precursors; that modification of each to the mature form correlated with phosphorylation; and that phosphorylation of the 69K precursor occurred more slowly than that of the 66K precursor, and resulted in a more dramatic slowing of its electrophoretic mobility. Second, comparisons of the 66K and 69K proteins based on partial proteolysis of [35S]methionine-labeled proteins, using V8 protease, and complete proteolysis of [32P]orthophosphate-labeled proteins, using trypsin or Pronase, provided no evidence of sequence relatedness. These analyses also suggested that the distribution of phosphorylated residues differs in the two proteins--clustered for the 69K and more disperse for the 66K. Phosphoamino acid analyses showed only phosphoserine in the 66K protein. The 69K protein contained, in addition to phosphoserine, an electrophoretically faster moving, unidentified spot. And third, immunological comparisons showed these proteins to exhibit little or no antigenic cross-reactivity. They did, however, demonstrate that the nuclear proteins are immunologically cross-reactive with their respective virion counterparts. Additional comparisons of these nuclear and virion proteins established that the virion 69K protein (v69) differs in electrophoretic mobility and net charge from the nuclear 69K protein but that it, as well as the virion 66K protein, has a two-dimensional phosphopeptide pattern similar to its nuclear counterpart.

Protein counterparts of human and simian cytomegaloviruses

Cytomegalovirus (CMV) proteins from isolates of both human (HCMV) and simian (SCMV) origin have been compared. Three classes were analyzed: the immediate-early (IE) proteins, other infected-cell-specific proteins not present in virus particles, and the proteins that constitute the mature extracellular virion. Comparisons were based on one- and two-dimensional (charge-size) separations in denaturing polyacrylamide gels, and on the selectivity of biosynthetic radiolabeling with [32P]orthophosphate and [3H]glucosamine. Results indicate that most, if not all, of the HCMV and SCMV proteins recognized, have counterparts in strain Colburn. As a group, the simian strains exhibit protein similarities that distinguish them from the human strains. Among the most diagnostic of these are the 205K and 145K virion proteins, each of which is about 7K smaller than its HCMV counterpart, and the predominant IE proteins, which are 10K to 20K (depending upon the strain) larger than their HCMV counterparts. The proteins of strain Colburn are shown to be more like those of the simian isolates than the human, and more like those of a vervet strain than rhesus. Leads provided by experiments using strain Colburn have aided in the identification of a previously unrecognized, abundant virion protein that is a principal phosphate acceptor, both in vivo and in vitro. Three additional phosphorylated proteins are identified in HCMV virions, as well as three glycoproteins. Only two HCMV strain-specific protein differences were detected by comparisons based on separation in SDS-containing polyacrylamide gels--one in the IE protein of strains Towne and Davis; the other in a virus capsid protein of strain AD169.

Host range transforming gene of polyoma virus plays a role in virus assembly

Polyoma virus host range transforming (hr-t) mutants are blocked in virion assembly. In normal 3T3 cells, a nonpermissive host, these mutants synthesize 30-40% as much viral DNA and 80-100% as much capsid proteins as does wild-type virus and yet produce only 1-2% as much infectious virus. Intermediates in virion assembly have been followed by [3H]thymidine incorporation. hr-t mutants synthesize 95S replicating minichromosomes, which accumulate as 75S forms. However, the latter fail to undergo efficient transition to 240S virion structures. This block in encapsidation is overcome in permissive hosts such as primary baby mouse kidney (BMK) epithelial cells. The block in assembly of 240S particles is accompanied by a failure to induce a series of acidic isoelectric forms of the major capsid protein, VP1. Multiple species of post-translationally modified VP1 are seen by two-dimensional gel electrophoresis in wild-type virus-infected cells. These acidic VP1 subspecies are decreased 6- to 10-fold in hr-t mutant-infected 3T3 cells but are produced in normal amounts when the same mutants infect BMK cells. When 3T3 cells are coinfected with hr-t mutant and wild-type viruses, normal amounts of the VP1 subspecies are present, and hr-t mutant viral DNA is efficiently packaged into virions. These studies demonstrate an important role of the hr-t gene of polyoma virus in virus assembly. Specifically, we propose that VP1 is a target for hr-t gene-controlled modification and that modified forms of VP1 are essential for encapsidation of viral minichromosomes.

Multiple proteins and subgenomic mRNAs may be derived from a single open reading frame on tobacco mosaic virus RNA

It has previously been shown that messenger activity for a protein of Mr = ca. 30k exists in RNA fractions extracted from particles of either native or alkali stripped U1 TMV, or from cowpea strain TMV, that are smaller than full genomic length. Analysis of sucrose gradient fractions containing this activity reveals a number of slightly smaller template activities directing synthesis of proteins between 18.5k and 29k in size. All of these messenger activities, including that for the 30k protein, respond to cap analogues in anomalous ways. Discrete RNA species that include active mRNAs for these proteins can be demonstrated in the same fractions by labelling with preparations of vaccinia capping enzyme and [alpha-32P] GTP without prior beta-elimination. Detailed analysis of three of these proteins (of Mr's ca. 30k, 29k and 23k) by peptide mapping and translation of purified vaccinia-labelled RNA demonstrates that all three are unrelated to the large early TMV proteins, but are related to each other in such a way as to form a nested set with staggered N termini and identical C termini. mRNAs of chain lengths ca. 1900 and 1500 bases direct synthesis of the 30k and 23k proteins respectively, an mRNA of about 1850 bases directs both 29k and (perhaps because of cross-contamination) 30k synthesis. Initiation codons for the 29k and 23k proteins have been mapped at positions 4960-4962 and 5191-5193 respectively on TMV RNA. Since all three encapsidated templates have similar properties we conclude that either there is a family of 30k-related proteins with unusual mRNAs, or that none of these in vitro translation products are directed by physiological templates.

Polyoma virus early and late mRNAs in productively infected mouse 3T6 cells

We mapped polyoma virus-specific mRNAs isolated from productively infected mouse 3T6 cells on the viral genome by analyzing nuclease S1-resistant RNA-DNA hybrids. The polyoma early mRNAs, which code for the three T antigens, have several 5' ends near 73 map units (m.u.). During the late phase of infection an additional 5' end is found near 71 m.u. All of the major early mRNAs have common 3' ends at 26.01 m.u. There is a minor species of early mRNA with a 3' end at 99.05 m.u. There are two proximal and two distal splice junctions in the early region which are used to generate three different spliced early mRNAs. There are three late mRNAs encoding the three virion proteins, VP1, VP2, and VP3. The late mRNAs have common 3' ends at 25.34 m.u. The late mRNAs have heterogeneous 5' leader sequences derived from the region between 65.53 and 68.42 m.u. The leader sequences are joined to the bodies of the messages coding for VP2, VP3, and VP1 at 66.59, 59.62, and 48.57 m.u., respectively. These results confirm and extend previous analyses of the fine structure of polyoma mRNAs.

Sequences at the capped 5'-ends of polyoma virus late region mRNAs: an example of extreme terminal heterogeneity

We have localized with respect to the genomic DNA sequence the capped 5'-termini of polyoma virus late region mRNAs. A minimum of fifteen different purine termini were found within a 94 base pair region (66.36 to 68.12 map units, nt 5075-5168) immediately preceding the sequence determining the late region mRNA leader repeat (1-3). The most common termini occur at nearly every possible purine within a 25 bp sequence proximal to the leader repeat unit. These do not bear the usual positional relationship to a sequence resembling the 'TATA' box consensus. Deletion mutants lacking minor cap sites and sequences upstream from the principal cap sites were viable. A deletion mutant lacking one of the principal cap sites formed small plaques, while a slightly larger deletion further impinging on the principal cap site region was non-viable. The principal cap sites, which we assume to be transcriptional initiation points, are included in a DNaseI hypersensitive region of polyoma virus chromatin (4).

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 of new proteins associated with the induction of interferon in human fibroblast cells

The relative amounts of translatable cellular mRNAs and newly synthesized cellular proteins were examined in poly(I) x poly(C)-induced human fibroblast cells early during induction. At this time interferon and interferon mRNA synthesis are maximal and cells have not acquired their antiviral thesis are maximal and cells have not acquired their antiviral state. Translation of the mRNA from poly(I) x poly(C)-induced cells in a wheat germ cell-free system led to the synthesis of a [35S]methionine-labeled 22,000-dalton protein that is precipitated by antiserum to highly purified human fibroblast interferon. The synthesis of this protein was detected only with the mRNA preparations that, when translated in Xenopus oocytes, coded for the synthesis of biologically active human interferon. Two-dimensional gel analysis of the [35S]methionine-labeled polypeptides translated from the total mRNA of the induced and uninduced cells revealed the presence of 23 new proteins that were translated from mRNAs of the induced cells but not from the mRNAs of the controls. These polypeptides ranged from 15,000 to 70,000 daltons. Thirteen of these proteins were detected in induced cells labeled with [35S]methionine. It is concluded that, in human fibroblasts, poly(I) x poly(C) induces, in addition to interferon, the synthesis of a variety of "interferon-associated" proteins.

Electron microscopic demonstration of the presence of amplified sequences at the 5'-ends of the polyoma virus late mRNAs

Electron microscopic techniques were used to examine the structure of the leader sequences at the 5'-ends of the late polyoma virus mRNAs. The three late mRNA's were partially purified and hybridized to an E. coli plasmid containing two polyoma virus genomes inserted in tandem. The hybrids were spread by the cytochrome c-formamide technique and visualized in the electron microscope. These studies revealed that whereas the body of a given mRNA molecule can hybridize with only one of the two corresponding body sequences in the two adjacent viral genomes, the leader of the same mRNA molecule can hybridize with both copies of the leader sequence-specific DNA. The mVP1 and mVP3 RNA species thus generated hybrids containing two loops, while mVP2 molecules formed hybrids containing one loop. Hence, the leaders of the three polyoma virus late mRNA species must contain two or more repeats of a sequence transcribed from a unique DNA segment. Length measurements showed that most leaders in the late mRNA's consist of at least 200 nucleotides and some contain up to 500 nucleotides, whereas the basic repeat sequence contains about 60 nucleotides.

Activation of an internal initiation site for protein synthesis during in vitro translation

The major mRNA for adenovirus 2 polypeptide pVIII sediments at 18S as assayed by in vitro translation in the messenger-dependent rabbit reticulocyte lysate system. However, a small amount of messenger activity for pVIII sediments at abut 27S, coincident with the mRNA for 100 K. Isolation and fractionation of poly(A) containing RNA following in vitro translation of 27S 100 K mRNA demonstrated the appearance of an 18S messenger activity for pVIII, which is approximately the size of the authentic mRNA for this protein. Partial degradation of 27S 100 K mRNA with alkali or ribonuclease T1 also results in activation of an 18S messenger activity for pVIII suggesting that in vitro messenger activity for pVIII associated with 27S RNA is due to degradation of 100 K mRNA during translation in the cell-free system.

Topography of the three late mRNA's of polyoma virus which encode the virion proteins

The three cytoplasmic polyadenylated mRNA's which separately encode the three capsid proteins (VP1, VP2, and VP3) of polyoma virus were mapped on the viral genome by one- and two-dimensional gel electrophoreses of nuclease S1-resistant RNA-DNA hybrids. The mRNA's, which we designated mVP1, mVP2, and mVP3 to indicate the coding functions deduced from the cosedimentation of the RNAs and the messenger activities, comprise an overlapping set of 3'-coterminal molecules which also share a heterogeneous family of noncoding 5'-terminal regions (Flavell et al., Cell 16:357--371, 1979; Legon et al., Cell 16:373--388, 1979). The three species differ in the length of the 3' colinear coding region which is spliced to the 5' leader sequences. The common polyadenylated 3' end maps at map unit 25.3. The 5' ends of the colinear bodies of mVP1, mVP3, and mVP2 map at 48.5, 59.5, and 66.5 map units, respectively. An examination of the polyoma virus DNA sequence (Arrand et al., J. Virol. 33:606--618, 1980) in the vicinities of splicing sites approximated by the S1 gel mapping data for sequences common to the ends of known intervening sequences allowed prediction of the precise splice points in polyoma virus late mRNA's. In all three cases, the leader sequences are joined to the mRNA bodies at least 48 nucleotides before the translational initiation codon used in each particular messenger. The start signal which functions in each mRNA is the first AUG (or GUG) triplet after the splice junction.

Polyoma virus DNA: complete nucleotide sequence of the gene which codes for polyoma virus capsid protein VP1 and overlaps the VP2/VP3 genes

The nucleotide sequence of part of the late region of the polyoma virus genome was determined. It contains coding information for the major capsid protein VP1 and the C-terminal region of the minor proteins VP2 and VP3. In the sequence with the same polarity as late mRNA's, all coding frames are blocked by termination codons in a region around 48 units on the physical map. This is the region where the N-terminus of VP1 and the C-termini of VP2 and VP3 have been located (T. Hunter and W. Gibson, J. Virol. 28:240-253, 1978; S. G. Siddell and A. E. Smith, J. Virol. 27:427-431, 1978; Smith et al., Cell 9:481-487, 1976). There are two long uninterrupted coding frames in the late region of polyoma virus DNA. One lies at the 5' end of the sequence and contains potential coding sequences for VP2 and VP3. The other contains 383 consecutive sense codons starting with the ATG at nucleotide position 1,218, extends from 47.5 to 25.8 units counterclockwise on the physical map, and is located where the VP1 gene has been mapped. The VP1 gene overlaps the genes for proteins VP2/VP3 by 32 nucleotides and uses a different coding frame. From the DNA sequence, the amino acid sequence of VP1 was predicted. The proposed VP1 sequence is in good agreement with other data, namely, with the partial N-terminal amino acid sequence and the total amino acid composition. The VP1 coding frame terminates with a TAA codon at 25.8 map units. This is followed by an AATAAA sequence, which may act as a processing signal for the viral late mRNA's. When both nucleotide and amino acid sequences are compared with their counterparts in the related simian virus 40, extensive homologies are found over the entire region of the two viral genomes. Maximum homology appears to occur in those regions which code for the C-termini of the VP1 proteins. The overlap region of VP1 with VP2/VP3 of polyoma virus is shorter by 90 nucleotides than is that of simian virus 40 and shows very limited homology with the simian virus 40 sequence. This leads to the suggestion that the overlap segments of both viruses have been freed from stringency imposed on drifting during evolution and that proteins VP2 and VP3 of polyoma virus may have been truncated by the appearance of a termination codon within the sequence.

Localization of three major cappe 5' ends of polyoma virus late mRNA's within a single tetranucleotide sequence in the viral genome

The nucleotide sequences at the 5' ends of polyoma virus late mRNA's were determined by direct RNA sequencing of decapped and 5'-(32)P-labeled RNase T1 oligoribonucleotides. Virus-specific polyadenylated cytoplasmic RNA, which was isolated from mouse cells late during productive infection, was enzymatically or chemically treated to specifically remove the cap structure (m(7)Gppp). The unblocked 5' ends of the viral mRNA's were then labeled enzymatically with (32)P, and the RNAs were digested with RNase T1 and fingerprinted. Three oligonucleotides derived from capped termini were isolated, and their sequences were determined to be pGmACAUUUUCUAUUUUAAGp, p(m)AmCAUUUUCUAUUUUAAGp, and p(m)AmUUUUCUAUUUUAAGp. These oligonucleotides comprise a staggered set with members 15, 17, and 18 nucleotides long, which share a common 3' sequence for 15 nucleotides. The sequences correspond exactly to the polyoma virus DNA sequence (Arrand et al., J. Virol. 33:606-618, 1980) from 66.79 to 66.46 map units (between 75 and 92 nucleotides preceding the ATG initiation codon for the capsid protein VP2). Previous results showed that the sequence between 13 and 64 nucleotides preceding the VP2 initiation codon corresponds to oligonucleotides reiterated in the leader sequence which is spliced onto the bodies of the three functionally distinct viral late mRNA's (Flavell et al., Cell 16:357-372, 1979; Legon et al., Cell 16:373-388, 1979). The three capped oligonucleotides we sequenced are derived from the first large predicted T1 oligonucleotide 5' to those detected in the leader sequence. The occurrence of a cap at each purine of a single tetranucleotide sequence reflects micro-heterogeneity either in transcriptional initiation or in processing cleavage involved in cap syntheses.

Partial amino-terminal sequences of the polyoma nonhistone proteins VP1, VP2, and VP3 synthesized in vitro

The three polyoma virus capsid proteins VP1, VP2, and VP3 were synthesized in vitro in the presence of several radiolabeled amino acids and, after purification on sodium dodecyl sulfate-polyacrylamide gels, were subjected to sequential Edman degradation. The partial amino-terminal amino acid sequences obtained were compared with the sequence of amino acids predicted from the polyoma virus DNA sequencing (Arrand et al., J. Virol. 33:606--618, 1980). Together, these results showed that the 5' ends of the VP1, VP2, and VP3 coding sequences are located 1,217, 289, and 634 nucleotides, respectively, from the junction of HpaII restriction fragments 3 and 5.

Morphogenetic genes C and Nu3 overlap in bacteriophage lambda

In bacteriophage lambda, genes C and Nu3, two of the four cistrons which are essential for normal prohead formation, have overlapping nucleotide sequences. These genes are translated in the same reading frame so that the Nu3 protein is identical to the COOH-terminal one-third of the C protein. This structural relationship may provide for the functional interaction of the C and Nu3 proteins through their regions of structural homology during prohead assembly. The in-phase overlapping organisation of genes may constitute a general strategy to facilitate the mutual interaction of a pair of proteins through their common structural domains.

Construction and analysis of viable deletion mutants of polyoma virus

Viable mutants of polyoma with small deletions ranging in size from 2 to 75 base pairs were obtained by infecting 3T3 cells with polyoma DNA that had been cleaved once with HaeII endonuclease or with DNase-Mn2+ digestion. The HaeII endonuclease-cleaved DNA yielded mutants with deletions at map position 72--73, whereas the mutants generated by DNase I-Mn2+ digestion had deletions either at map position 72--73 or within the map coordinates 92 and 99. Both groups of mutants appeared to grow as well as wild-type virus in 3T3 cells. The deletions at map position 72--73 did not alter the virus's ability to transform rat cells. Hence, the region just to the early side of the origin of DNA replication is not essential for vegetative growth or transformation. But the mutants with deletions in the region between map coordinates 92 and 99, a segment thought to code for polyoma large and middle T antigens (Hutchinson et al., Cell 15:65--77, 1978; Smart and Ito, Cell 15:1427--1437, 1978; Soeda et al., Cell 17:357--370, 1979), transformed rat cells at 0.2 to 0.05 the efficiency of wild-type virus.

Cell-free translation of simian virus 40 16S and 19S L-strand-specific mRNA classes to simian virus 40 major VP-1 and minor VP-2 and VP-3 capsid proteins

Simian virus 40 capsid proteins VP-1, VP-2, and VP-3 have been synthesized in wheat germ and reticulocyte cell-free systems in response to either poly(A)-containing mRNA from the cytoplasm of infected cells or viral RNA purified by hybridization to simian virus 40 DNA linked to Sepharose. All three viral polypeptides synthesized in vitro are specifically immunoprecipitated with anti-simian virus 40 capsid serum. VP-2 and VP-3 are related by tryptic peptide mapping to each other but not to VP-1. The most abundant class of L-strand-specific viral mRNA, the 16S species, codes for the major capsid protein. The relatively minor 19S class directs the cell-free synthesis of VP-1, VP-2, and VP-3. Whether the 19S RNA represents more than one distinct species of mRNA is not yet clear. VP-1 mRNA can be isolated from the cytoplasm, detergent-washed nuclei, and the nuclear wash fraction. The mRNA from the nuclear wash fraction is enriched for VP-2 mRNA when compared to other viral or cellular polypeptides.

Translation of polyoma virus T antigens in vitro

Polyoma virus-specific RNA isolated from the cytoplasm of lytically infected cells can be translated in vitro to yield three T antigens, of Mrs approximately 90,000, 60,000, and 22,000. The tryptic peptide patterns of the T antigens synthesized in vitro are similar or identical to the patterns of the corresponding proteins in polyoma-infected cells. All three proteins incorporate methionine donated from initiator tRNA in vitro. Polyoma cRNA codes for a protein that is slightly larger than the 22,000 T antigen and that, by other criteria, is similar to the 22,000 T antigen. Translation of cRNA does not yield the 90,000 and 60,000 T antigens, suggesting that the generation of the mRNAs for these T antigens requires the removal of intervening sequences. The mRNA for the 90,000 T antigen is smaller than the mRNAs for the 22,000 and 60,000 proteins. All three proteins share common NH2-terminal sequences, and the 60,000 T antigen may be translated partially in a different reading frame from sequences also coding for the 90,000 T antigen. The demonstration that polyoma virus codes for three different T antigens raises the possibility that all three proteins may be involved in cell transformation.