Heterogeneity and 5'-terminal structures of the late RNAs of simian virus 40

A transcription factor from simian virus 40 chromosomes which activates the viral late promoter in vitro

We have characterized a transcription factor, obtained from simian virus 40 (SV40) chromosomes, which activates transcription from the SV40 late promoter in vitro. The late promoter-activating factor was distinct from SV40 T antigen as judged by its behavior on chromatography on hydroxylapatite; it was not recognized by anti-T antibodies, while T antigen itself was recognized. T antigen from SV40 chromosomes, on the other hand, abolished transcription in vitro from the early promoter. In DNase I footprinting experiments, a partially purified late promoter-activating factor preparation protected a region of DNA centered on SV40 nucleotide 270, which is between the repeated 72-base-pair enhancer and the major late RNA start site. Proteins from HeLa cells did not give the same footprint at this position. Gel mobility shift assays showed that proteins from SV40-infected CV-1 cells form a complex with DNA containing this binding site. The complex has a different rate of gel migration and a higher stability than complexes formed with proteins from uninfected cells.

Expression of the gene encoding the 17-kilodalton antigen from Rickettsia rickettsii: transcription and posttranslational modification

Recently, we reported the molecular cloning and nucleotide sequence analysis of a gene from Rickettsia rickettsii that codes for a 17-kilodalton antigen (17K antigen) and is preceded by sequences closely resembling the -10 and -35 consensus sequences for recognition by Escherichia coli RNA polymerase (Anderson et al., J. Bacteriol. 169:2385-2390, 1987). Experiments described in this report indicate that the start sites for initiating transcription of the 17K antigen gene are identical in the E. coli clone and in intact R. rickettsii. In each case, initiation was shown to begin 9 bases downstream of the presumed Pribnow box sequence (TATACT). A 169-base-pair fragment containing the promoter sequence initiated transcription in both directions when cloned into an E. coli promoter probe vector. The rickettsial fragment was found to contain sequences identical to the -10 region (but not the -35 region) of the E. coli promoter consensus sequence directed away from the 17K antigen gene. The amino-terminal portion (residues 17 to 20) of the deduced amino acid sequence for the 17K antigen contained the tetrapeptide Leu-Gln-Ala-Cys, a sequence that conforms favorably to those described for lipid modification and cleavage by lipoprotein signal peptidase II. The 17K antigen produced by the E. coli clone was shown to be labeled with [3H]palmitate and [3H]glycerol, indicative of lipid modification. In vitro mutagenesis designed to alter the cysteine at residue 20 to a glycine abolished incorporation of [3H]palmitate, suggesting that posttranslational modification occurs via a mechanism similar to that described for other gram-negative bacterial lipoproteins.

Organization and structure of Volvox beta-tubulin genes

Genomic clones encoding two Volvox beta-tubulin genes have been isolated and shown to represent the only two beta-tubulin genes in the genome. Restriction fragment length polymorphism analysis was used to demonstrate that the two genes are genetically linked. One of these genes was sequenced and the mRNA start site(s) determined by primer extension. A comparison of its sequence to those of the two beta-tubulin genes of Chlamydomonas revealed: (1) a high degree of conservation of the coding region, with the predicted amino acid sequence differing only in the C-terminal residue; (2) extensive sequence conservation in the 5' untranslated leader region and a 16 bp (putative regulatory) sequence in the promoter region; (3) the same number and location of introns, with a short region of homology in intron 1, but little significant homology in introns 2 and 3.

Organization and structure of Volvox alpha-tubulin genes

Southern analysis of Volvox genomic DNA revealed two genes homologous to Chlamydomonas reinhardtii alpha-tubulin cDNA. Restriction fragment length polymorphism analysis indicated that the two genes are not genetically linked. Clones representing one of the alpha-tubulin genes have been isolated from a genomic library of Volvox carteri f. nagariensis. A 3153 bp BamHI fragment containing the entire alpha-tubulin gene (1802 bp) plus 707 bp of the 5'- and 644 bp of the 3'-untranslated regions has been sequenced, revealing the following features: (1) the derived alpha-tubulin primary structure of 451 amino acids is highly conserved, differing in two residues from the alpha 1- and in two additional residues from the alpha 2-tubulin of C. reinhardtii; (2) in comparison to the C. reinhardtii genes, the Volvox alpha-tubulin gene contains a third intron; positions of the other two introns are precisely conserved; (3) codon usages are biased towards G or C, and against A, in the third position; 19 codons are absent from the alpha-tubulin coding sequence, and 5 of these are not used in any of 7 compiled Volvox genes; (4) transcription begins with an A, 30 bp downstream of the putative TATA box; upstream of the TATA box is a 14 bp sequence similar to consensus sequences found in all 4 C. reinhardtii tubulin genes and believed to regulate promoter function.

An excised SV40 intron accumulates and is stable in Xenopus laevis oocytes

Xenopus laevis oocytes injected with simian virus 40 (SV40) DNA synthesize abundant quantities of viral late region RNA. In a previous analysis of the 5' ends of oocyte SV40 late RNAs, it was observed that, in contrast to the majority of the late RNA species, an abundant class of viral late RNAs, whose 5' ends mapped at or near nucleotide 294, was not polyadenylated. The structure of this RNA class has now been characterized further. We have shown that this species consists of a class of small uncapped RNA molecules with heterogeneous 3' ends mapping between nucleotides 417 and 433. This corresponds well with the position of a 139-nucleotide intron within the leader region of late 16S RNA (nucleotides 294-433). The identification of this RNA class as an excised intron was strongly supported by the fact that it displayed anomalous mobilities on different percentage polyacrylamide gels, a property of lariat introns. Furthermore, incubation of oocyte RNA with a HeLa cell extract with lariat debranching activity converted the small RNA to a class that now migrated as less than or equal to 140 nucleotides in length in 8% gels, consistent with the size of the linear intraleader intron. Additional analysis of this RNA showed that it is primarily nuclear in localization and is probably the most stable viral RNA species in the oocyte. These data suggest that oocytes accumulate large quantities of the 16S intraleader intron because of their failure to debranch this RNA efficiently.

Transcription elongation factor SII interacts with a domain of the large subunit of human RNA polymerase II

Genomic sequences for the large subunit of human RNA polymerase II corresponding to a part of the fifth exon were inserted into an expression vector at the carboxy-terminal end of the beta-galactosidase gene. The in-frame construct produced a 125-kilodalton fusion protein, containing approximately 10 kilodaltons of the large subunit of RNA polymerase II and 116 kilodaltons of beta-galactosidase. The purified bacterially produced fusion protein inhibited specific transcription from the adenovirus type 2 major late promoter, while beta-galactosidase had no effect. This effect of the fusion protein was during RNA elongation, not at the level of initiation, resembling the faithfully initiated but incomplete transcripts produced with purified factors in the absence of SII. Similarly, monoclonal antibody 2-7B, which reacts with the RNA polymerase II region represented in the fusion protein, inhibited specific transcription at the level of elongation in a whole-cell extract. Both monoclonal antibody 2-7B and the fusion protein, although unable to inhibit purified RNA polymerase II in a nonspecific transcription assay, selectively blocked the stimulation elicited by transcription elongation factor SII on the activity of the purified enzyme in vitro. This suggests that the fusion protein traps the SII in nonstimulatory interactions and that antibody 2-7B inhibits SII binding to RNA polymerase II. Thus, this suggests that an SII-binding contact required for specific RNA elongation resides within the fifth exon region of the largest RNA polymerase II subunit.

Simian virus 40 major late promoter: a novel tripartite structure that includes intragenic sequences

Unlike most genes transcribed by RNA polymerase II, the simian virus 40 late transcription unit does not have a TATA box. To determine what sequences are required for initiation at the major late mRNA cap site of simian virus 40, clustered point mutations were constructed and tested for transcriptional activity in vitro and in vivo. Three promoter elements were defined. The first is centered 31 base pairs upstream of the cap site in a position normally reserved for a TATA box. The second is at the cap site. The third occupies a novel position centered 28 base pairs downstream of the cap site within a protein-coding sequence. The ability of RNA polymerase II to recognize this promoter suggests that there is greater variation in promoter architecture than had been believed previously.

Simian virus 40 T antigen alters the binding characteristics of specific simian DNA-binding factors

The late promoter of simian virus 40 is transcriptionally activated, in trans, by large T antigen, the primary viral early gene product. Although large T antigen is a well-characterized DNA-binding protein, a variety of data suggest that its trans-activation function does not require direct interaction with DNA. We demonstrate that defined late promoter elements, omega (omega), tau (tau), and delta (delta), necessary for T-antigen-mediated trans-activation, are binding sites for simian cellular factors, not T antigen. Two of the late promoter elements (omega and tau) are shown to bind the same factor or family of factors. These factors bind to a site very similar to that for the HeLa cell factor AP1. We refer to these factors as the simian AP1-sequence recognition proteins (sAP1-SRPs). Compared with normal simian CV-1P cells, the sAP1-SRPs from T-antigen-producing COS cells, or from 14-h simian virus 40-infected CV-1P cells, showed altered binding patterns to both the omega and tau binding sites. In addition, the sAP1-SRPs from T-antigen-containing cells bound to the tau site more stably than did the analogous factors from normal CV-1P cells. The altered pattern of binding and the increased stability of binding correlated with the presence of T antigen in the cell. Additionally, the alteration of the binding pattern within 14 h of infection in CV-1P cells is temporally correct for late promoter activation. Overall, the data show (i) that the late promoter elements necessary for T-antigen-mediated trans-activation contain binding sites for simian cellular DNA-binding proteins; (ii) that the presence of T antigen causes alterations in the binding characteristics of specific simian cellular DNA-binding factors or families of factors; and (iii) that factors which bind to the late promoter elements required for activation have altered and more stable binding characteristics in the presence of T antigen. These points strongly suggest that T antigen mediates trans-activation indirectly through the alteration of binding of at least one specific simian cellular factor, sAP1-SRP, or through the induction of a family of sAP1-SRP factors.

Use of RNase H and primer extension to analyze RNA splicing

A new method for the characterization of pre-mRNA splicing products is presented. In this method RNA molecules are hybridized to an oligodeoxynucleotide complementary to exon sequences upstream of a given 5' splice site, and the RNA strands of the resulting RNA:DNA hybrids are cleaved by RNase H. The cleaved RNAs are then subjected to primer extension using a 32P-labelled primer complementary to exon sequences downstream of an appropriate 3' splice site. Since the primer extension products all terminate at the site of RNase H cleavage, their lengths are indicative of the splice sites utilized. The method simplifies the study of the processing of complex pre-mRNAs by allowing the splicing events between any two exons to be analyzed. We have used this approach to characterize the RNAs generated by expression of the rat tropomyosin 1 (Tm 1) gene in various rat tissues and in cultured cells after transient transfection. The results demonstrate that this method is suitable for the analysis of alternative RNA processing in vivo.

Structure and expression of the ompB operon, the regulatory locus for the outer membrane porin regulon in Salmonella typhimurium LT-2

The ompB operon of Salmonella typhimurium encodes a positive transcriptional regulator OmpR and an inner membrane protein EnvZ. Both proteins are needed for the proper expression of the outer membrane proteins OmpC and OmpF. We have determined the nucleotide sequence of the ompB locus and its adjacent regions. A comparison between the S. typhimurium and Escherichia coli sequences revealed that the ompB locus is highly conserved. The sequence data also showed that ompR and envZ form an operon, where the coding regions overlap by four base-pairs. Utilizing ompR-lacZ and envZ-lacZ gene fusions, the translational levels of expression of these two genes were measured, showing that ompR is considerably more efficiently expressed than envZ. Analysis of ompR frameshift mutations showed that translation of envZ is almost totally dependent on the translation of the upstream gene ompR. The mechanism of this translational coupling appears to be a reinitiation of the ribosome at the overlapping region of the two genes. The characteristics of the OmpR and EnvZ proteins were in agreement with the known functions and cellular locations of these proteins. OmpR was found to contain a putative DNA binding site, while EnvZ contained two hydrophobic stretches typical of transmembrane regions. Both OmpR and EnvZ show extensive homologies with many proteins from a number of different origins, all of which function in pairs and through which environmental signals modulate gene expression. Hence, the tightly coupled synthesis of these proteins seems to be essential in eliciting a proper response in the transmembrane regulation of gene expression.

Simian virus 40 major late promoter: a novel tripartite structure that includes intragenic sequences

Unlike most genes transcribed by RNA polymerase II, the simian virus 40 late transcription unit does not have a TATA box. To determine what sequences are required for initiation at the major late mRNA cap site of simian virus 40, clustered point mutations were constructed and tested for transcriptional activity in vitro and in vivo. Three promoter elements were defined. The first is centered 31 base pairs upstream of the cap site in a position normally reserved for a TATA box. The second is at the cap site. The third occupies a novel position centered 28 base pairs downstream of the cap site within a protein-coding sequence. The ability of RNA polymerase II to recognize this promoter suggests that there is greater variation in promoter architecture than had been believed previously.

Functional anatomy of the simian virus 40 late promoter

We have examined the control sequences for the late promoter function of simian virus 40 (SV40) in COS-1 cells which produce SV40 T antigen constitutively. Plasmids were constructed by cloning mutant late promoter segments upstream from sequences coding for the bacterial chloramphenicol acetyltransferase (CAT) gene, and were converted to "double-origin" type by inserting functional replication origin segments downstream from the CAT gene for replicative competence when necessary. The late promoter activity was determined by transient expression assay of the CAT mRNA and enzyme activity levels following DNA-mediated gene transfer into COS-1 cells. We find that the minimal replication origin and the 21-bp repeat containing T antigen and transcription factor Sp1 binding sites, respectively, are dispensable for late promoter function provided that one copy of the 72-bp repeat enhancer is present. We have mapped within the 72-bp repeat the major late promoter component in a 68-bp fragment (located between nucleotides 205 and 272), and found an overlapping 55-bp fragment (located between nucleotides 179 and 234) to have about one-fifth of the late promoter activity. Both the 68- and 55-bp fragments lack some of the core sequence elements required of the 72-bp repeat for transcriptional enhancer activity, and lack the ability to enhance the activity of the SV40 early promoter. The results suggest that the organization of functional units of the 72-bp repeat required for transcriptional enhancement of the early promoter is different from that required for late promoter function. The 21-bp repeat was found to have some late promoter activity located within the origin-distal copy in the absence of the 72-bp repeat. In association with the 21-bp repeat, the otherwise dispensable origin-proximal 22-bp of the 72-bp repeat containing activator protein AP-1 binding site augmented late promoter activity by three- to fourfold.

Simian virus 40 T antigen alters the binding characteristics of specific simian DNA-binding factors

The late promoter of simian virus 40 is transcriptionally activated, in trans, by large T antigen, the primary viral early gene product. Although large T antigen is a well-characterized DNA-binding protein, a variety of data suggest that its trans-activation function does not require direct interaction with DNA. We demonstrate that defined late promoter elements, omega (omega), tau (tau), and delta (delta), necessary for T-antigen-mediated trans-activation, are binding sites for simian cellular factors, not T antigen. Two of the late promoter elements (omega and tau) are shown to bind the same factor or family of factors. These factors bind to a site very similar to that for the HeLa cell factor AP1. We refer to these factors as the simian AP1-sequence recognition proteins (sAP1-SRPs). Compared with normal simian CV-1P cells, the sAP1-SRPs from T-antigen-producing COS cells, or from 14-h simian virus 40-infected CV-1P cells, showed altered binding patterns to both the omega and tau binding sites. In addition, the sAP1-SRPs from T-antigen-containing cells bound to the tau site more stably than did the analogous factors from normal CV-1P cells. The altered pattern of binding and the increased stability of binding correlated with the presence of T antigen in the cell. Additionally, the alteration of the binding pattern within 14 h of infection in CV-1P cells is temporally correct for late promoter activation. Overall, the data show (i) that the late promoter elements necessary for T-antigen-mediated trans-activation contain binding sites for simian cellular DNA-binding proteins; (ii) that the presence of T antigen causes alterations in the binding characteristics of specific simian cellular DNA-binding factors or families of factors; and (iii) that factors which bind to the late promoter elements required for activation have altered and more stable binding characteristics in the presence of T antigen. These points strongly suggest that T antigen mediates trans-activation indirectly through the alteration of binding of at least one specific simian cellular factor, sAP1-SRP, or through the induction of a family of sAP1-SRP factors.

Interferon-responsive regulatory elements in the promoter of the human 2',5'-oligo(A) synthetase gene

The interferon (IFN)-activated human 2',5'-oligo(A) synthetase E gene contains 11 RNA starts and lacks TATA and CAAT signals. DNA sequences around the promoter make the expression of the chloramphenicol acetyltransferase gene (CAT) inducible over 20-fold by IFN. A 72-base-pair segment (E-IRS) immediately upstream of the RNA starts was defined as being required for IFN-activated expression of the E-gene promoter-CAT constructs and acts in a position-independent manner. It also confers IFN-activated enhancement to the herpes simplex virus thymidine kinase promoter. On this promoter, the 5' part of the E-IRS functions as a constitutive enhancer, while the last 16 base pairs of the E-IRS is sufficient to give IFN-induced expression. On the E-gene promoter, the constitutive enhancer and the IFN-activated sequence are both needed but can be separated. In addition, promoter competition experiments indicate a third regulatory region which helps to repress expression of the E gene in uninduced cells.

Messenger RNAs of a strongly-expressed late gene of cowpox virus contain 5'-terminal poly(A) sequences

We have identified and characterized one of the most strongly-expressed genes of cowpox virus (CPV). This is the gene encoding the major protein component of the A-type inclusion bodies produced by this virus. This gene (designated the 160K gene) is transcribed late during the infection. Analyses of its mRNAs showed that these late RNAs, unlike all other characterized late mRNAs of poxviruses, are uniform in length. However, the most remarkable feature of the mRNAs of the 160K gene is the structure of their 5'-termini. Most of these mRNAs have 5'-terminal poly(A) sequences containing 5-21 residues. Furthermore, these 5'-terminal poly(A) sequences are not complementary to the corresponding region of the template strand of the viral DNA. Instead, the nucleotide sequences of the mRNA and the viral DNA diverge at the site of the three As in the sequence 5'-TAAATG-3' containing the gene's initiation codon. Consequently, the poly(A) provides the leader sequences of these mRNAs. These unusual 5'-terminal structures suggest that the late mRNAs of pox-virus genes are generated by a novel process.

Mechanisms of synthesis of virion proteins from the functionally bigenic late mRNAs of simian virus 40

The late 19S RNAs of simian virus 40 (SV40) are functionally polycistronic, i.e., all encode both VP2 and VP3. The VP3-coding sequences are situated in the same reading frame as the VP2-coding sequences, within the carboxy-terminal two-thirds of the VP2-coding sequences. To test whether VP3 is produced by proteolytic processing of VP2, we introduced a variety of deletion and insertion mutations within the amino-terminal end of the VP2-coding sequences. Genetic and biochemical analysis of the proteins synthesized in cells transfected with these mutants indicated that VP2 and VP3 were synthesized independently of each other. A leaky scanning model for the synthesis of VP3 was tested by the insertion of a strong initiation signal (CCAACATGG) upstream of the VP3-coding sequences. When the signal was placed in the same reading frame as VP3, synthesis of VP3 was reduced by a factor of 10 to 20, whereas synthesis of the expected VP3-related fusion protein occurred at a rate similar to that observed for VP3 in cells transfected with wild-type SV40 DNA. Insertion of this strong initiation signal at the same site, but in a different reading frame, resulted in the synthesis of VP3 at one-third of the wild-type rate. Mutation of the VP2 initiator AUG resulted in a small but reproducible (1.6-fold) increase in VP3 accumulation. From these experiments we conclude that (i) VP3 is synthesized predominantly by independent initiation of translation via a leaky scanning mechanism, rather than by proteolytic processing of VP2 or direct internal initiation of translation; (ii) a strong initiation signal 5' of the VP3-coding sequences can significantly inhibit synthesis of VP3, but does not act as an absolute barrier to scanning ribosomes; (iii) approximately 70% of scanning ribosomes bypass the VP2 initiator AUG, which is present in a weak context (GGUCCAUGG), and initiate at the VP3 initiation signal located downstream; and (iv) reinitiation of translation appears to occur on the SV40 late 19S mRNAs at an efficiency of 25 to 50%.

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.

The late spliced 19S and 16S RNAs of simian virus 40 can be synthesized from a common pool of transcripts

The late transcripts from the simian virus 40 (SV40) are alternatively spliced into two classes of spliced RNAs, 19S and 16S in size. We are interested in understanding the precursor-product relationships that result in the excision of different intervening sequences (introns) from the late transcripts. SV40 mutants containing precise deletions of the introns for each of the spliced 19S and 16S RNA species, including a previously undetected doubly spliced 19S RNA species, were isolated. Analysis by S1 mapping and a modified primer extension technique of the viral RNAs made in monkey cells transfected with each of these mutants led to the following conclusions. (i) Spliced late 19S RNA is not an intermediate in the synthesis of the late 16S RNAs. (ii) The 3' splice site used in the synthesis of the late 16S RNAs can join, albeit inefficiently, with alternative 5' splice sites in the absence of the 5' splice site normally used to synthesize 16S RNA. (iii) There is no obligatory order of excision of introns in the formation of the doubly spliced SV40 late 19S and 16S RNA species. A mutant was constructed by site-directed mutagenesis in which the 5'-proximal 3' splice site used in the synthesis of the doubly spliced RNAs is inactive. Cells transfected with this mutant processed transcripts into 19S RNA which, in wild-type-transfected cells, would have become doubly spliced 16S RNA. Therefore, we conclude that some of the spliced late 19S and 16S RNA can be synthesized from a common pool of transcripts.

Interferon-responsive regulatory elements in the promoter of the human 2',5'-oligo(A) synthetase gene

The interferon (IFN)-activated human 2',5'-oligo(A) synthetase E gene contains 11 RNA starts and lacks TATA and CAAT signals. DNA sequences around the promoter make the expression of the chloramphenicol acetyltransferase gene (CAT) inducible over 20-fold by IFN. A 72-base-pair segment (E-IRS) immediately upstream of the RNA starts was defined as being required for IFN-activated expression of the E-gene promoter-CAT constructs and acts in a position-independent manner. It also confers IFN-activated enhancement to the herpes simplex virus thymidine kinase promoter. On this promoter, the 5' part of the E-IRS functions as a constitutive enhancer, while the last 16 base pairs of the E-IRS is sufficient to give IFN-induced expression. On the E-gene promoter, the constitutive enhancer and the IFN-activated sequence are both needed but can be separated. In addition, promoter competition experiments indicate a third regulatory region which helps to repress expression of the E gene in uninduced cells.

Contribution of different GC-motifs to the control of simian virus 40 late promoter activity

During the course of lytic infection the 21-bp repeat region regulates differentially the late gene expression; a mutant deleted for this region expresses late genes either to a higher level in the absence of T antigen or to a lower level in the late phase of infection as compared to wild type (23). By analysing a series of clustered point mutations generated within the GC-motifs we show that i) mutations within motifs I and II stimulate late transcription two to three-fold, suggesting that competition for transcription machinery between early-early and late promoters is mediated by these two motifs, ii) after viral replication, simultaneous mutations within motifs IV, V and VI decrease to 23% the efficiency of late transcription, indicating that these motifs are elements of the late promoter. Moreover comparison of results presented in this paper with results published by Barrera-Saldana et al. strongly suggest that late-early and late promoters are regulated in a similar manner.

Missense mutations in the VP1 gene of simian virus 40 that compensate for defects caused by deletions in the viral agnogene

Simian virus 40 mutants lacking sequences in the late leader region are viable but produce smaller plaques than does wild-type virus. Within three passages at low multiplicities of infection, virus stocks of several such mutants accumulated variants that synthesized an altered form of the major virion protein, VP1, having a slightly faster mobility in sodium dodecyl sulfate-polyacrylamide gels than did the wild-type protein. Because these variants overgrew the original virus stocks, we consider them to be second-site revertants. By construction and characterization of a series of recombinants, the second-site mutations were shown to map to at least two different regions of the VP1 gene. Nucleotide sequence analysis indicated that single-amino-acid changes were responsible for the rapid mobility of VP1. When combined in cis with either a wild-type or mutant leader region, these VP1 mutations sped up by 10 to 20 h the time course of accumulation of infectious progeny but not of viral DNA or VP1. LP1, the protein encoded by the agnogene, was shown previously to be necessary for the efficient transport of the virion proteins to the nucleus or for their efficient assembly with viral minichromosomes. The VP1 missense mutations reported here compensate for the lack of LP1 by facilitating this process. On the basis of these findings and findings reported previously by us and others, we hypothesize that LP1 facilitates the formation of infectious particles by inhibiting the polymerization of VP1 molecules until the time they interact with viral minichromosomes; the VP1 mutations reported here compensate for the loss of LP1 by lessening the potential of VP1 for self-polymerization.

Specific stimulation of simian virus 40 late transcription in vitro by a cellular factor binding the simian virus 40 21-base-pair repeat promoter element

We have identified a cellular transcription factor from uninfected HeLa cells that stimulates the simian virus 40 (SV40) late mode of transcription and specifically binds the SV40 21-base-pair repeat promoter element. In particular, the late SV40 transcription factor (LSF) stimulates transcription at initiation sites L325 and L264 of the SV40 late promoter, which are the major transcription sites utilized after DNA replication during the SV40 lytic cycle. In addition, LSF appears to stimulate transcription to a lesser extent from the late-early initiation site of the early promoter. LSF binds specifically to the 21-base-pair repeats of the SV40 promoters, forming specific protein-DNA complexes, which migrate more rapidly through nondenaturing polyacrylamide gels than that formed by the previously identified transcription factor Sp1. Thus, LSF is distinguishable from Sp1 in both its transcriptional and DNA-binding properties. These findings suggest a potential role of LSF in the early to late transcriptional switch during a SV40 lytic infection.

Identification of the major cottontail rabbit papillomavirus late RNA cap site and mapping and quantitation of an E2 and minor E6 coding mRNA in papillomas and carcinomas

The capsite of the 2.6- and 4.8-kb major late transcripts of cottontail rabbit papillomavirus (CRPV) has been mapped by primer extension. A leader exon of about 300 nucleotides common to both RNAs is located in the untranslated region of the genome upstream of the capsites for early transcripts. In contrast to the early capsites which are all preceded by TATA boxes, no such sequence is present 30 nucleotides upstream of the late capsite. These data indicate that the switch from early to late transcription involves recognition of a new promoter and suppression of transcription termination at the early polyadenylation site. We have also identified a minor exon with a coding potential for a putative E2 transactivating protein. Quantitation by S1 mapping of the E2 coding exon and a minor exon coding for a full-sized E6 protein unique in size to the highly oncogenic CRPV did not reveal differences in the level of transcription between papillomas and carcinomas.

Developmental regulation of DNase I-hypersensitive sites in Dictyostelium discoideum

We have studied two regions of Dictyostelium discoideum chromatin and identified several DNase I-hypersensitive sites in these regions. One of these sites is located about 300 to 500 bases upstream of the transcriptional start site of a gene that is expressed at all stages of development. This site is present in both vegetative cells and postaggregation cells. Another hypersensitive site is associated with a gene that is expressed only after the multicellular stage. This site is located about 400 bases upstream of the start site, and it is present only in postaggregation cells. Thus, much like higher eucaryotes, D. discoideum contains DNase I-hypersensitive sites that may be involved in the regulation of the genes with which they are associated.

Nucleotide sequences of liver, lachrymal, and submaxillary gland mouse major urinary protein mRNAs: mosaic structure and construction of panels of gene-specific synthetic oligonucleotide probes

The mouse major urinary proteins (MUPs) are encoded by a gene family of about 35 to 40 members. MUPs are synthesized in at least six secretory tissues under a variety of developmental and endocrine controls, but the identities of the individual genes expressed in each tissue have not previously been established. In this article, we present the nucleotide sequences of five MUP mRNAs which we designate MUP I through V. MUPs I, II, and III are the most abundant MUP mRNA species in the liver, and MUPs IV and V are the most abundant MUP mRNA species in the lachrymal gland and the submaxillary gland, respectively. The sequence data show that each of the five mRNAs is encoded by a distinct member of the gene family. The structures of the MUP mRNA consist of interspersed segments of variable and conserved sequences. On the basis of the sequences of the variable segments, gene-specific panels of synthetic oligonucleotide probes were prepared. The gene-specific panels were used to identify cloned genes and, as described in the accompanying paper (K. Shahan, M. Denaro, M. Gilmartin, Y. Shi, and E. Derman, Mol. Cell. Biol. 7:1947-1954, 1987), to characterize the expression of MUP genes I through V.

Primer extension analysis of tRNA gene transcripts synthesized in vitro and in vivo

The primer elongation method has been adapted to analyze tRNA gene transcripts. The primer used to direct cDNA synthesis from a corresponding tRNA template, in the presence of AMV reverse transcriptase, was a restriction fragment, or a synthetic oligonucleotide, containing exclusively coding nucleotides of a tRNA gene. This method not only allows one to identify the exact 5'-end of mature tRNA, but also 5'-ends of primary transcripts are readily determined. Further, analysis of tRNAs synthesized in vitro, as well as tRNAs produced in vivo in homologous and heterologous organisms can be studied. Purification of the tRNAs questioned, from bulk tRNA, is not necessary.

Developmental regulation of DNase I-hypersensitive sites in Dictyostelium discoideum

We have studied two regions of Dictyostelium discoideum chromatin and identified several DNase I-hypersensitive sites in these regions. One of these sites is located about 300 to 500 bases upstream of the transcriptional start site of a gene that is expressed at all stages of development. This site is present in both vegetative cells and postaggregation cells. Another hypersensitive site is associated with a gene that is expressed only after the multicellular stage. This site is located about 400 bases upstream of the start site, and it is present only in postaggregation cells. Thus, much like higher eucaryotes, D. discoideum contains DNase I-hypersensitive sites that may be involved in the regulation of the genes with which they are associated.

Nucleotide sequences of liver, lachrymal, and submaxillary gland mouse major urinary protein mRNAs: mosaic structure and construction of panels of gene-specific synthetic oligonucleotide probes

The mouse major urinary proteins (MUPs) are encoded by a gene family of about 35 to 40 members. MUPs are synthesized in at least six secretory tissues under a variety of developmental and endocrine controls, but the identities of the individual genes expressed in each tissue have not previously been established. In this article, we present the nucleotide sequences of five MUP mRNAs which we designate MUP I through V. MUPs I, II, and III are the most abundant MUP mRNA species in the liver, and MUPs IV and V are the most abundant MUP mRNA species in the lachrymal gland and the submaxillary gland, respectively. The sequence data show that each of the five mRNAs is encoded by a distinct member of the gene family. The structures of the MUP mRNA consist of interspersed segments of variable and conserved sequences. On the basis of the sequences of the variable segments, gene-specific panels of synthetic oligonucleotide probes were prepared. The gene-specific panels were used to identify cloned genes and, as described in the accompanying paper (K. Shahan, M. Denaro, M. Gilmartin, Y. Shi, and E. Derman, Mol. Cell. Biol. 7:1947-1954, 1987), to characterize the expression of MUP genes I through V.

Use of an in vitro tuberization system to study tuber protein gene expression

Nodal cuttings from micropropagated potato plantlets give rise to microtubers when placed on Murashige and Skoog medium containing 6% sucrose and 2.5 mg/liter kinetin and incubated in the dark at 19 degrees C. Microtubers produced from the cultivar Superior were shown to contain the same characteristic group of proteins as field-grown tubers. As with field-grown tubers, the 40,000-dalton major tuber glycoprotein, patatin, accumulated to high levels in microtubers, reaching 3.7 +/- 0.2 mg/g fresh weight after 90 d. Also in agreement with field-grown plants, stems and leaves of micropropagated plantlets did not contain detectable levels of patatin, but small amounts of an electrophoretically distinct form accumulated transiently in roots. Patatin mRNA is readily detectable in developing microtubers 15 d after transfer of the cuttings to inductive medium. Patatin mRNA was also present in roots, but as with field-grown plants, was 50- to 100-fold less abundant and could be distinguished from that in tubers by primer extension. Microtuber development and patatin accumulation were inhibited by gibberellic acid.

The sequence motifs that are involved in SV40 enhancer function also control SV40 late promoter activity

The simian virus 40 (SV40) enhancer element is constituted of two domains which contain sequences important for late transcription (M. Ernoult-Lange, F. Omilli, D. O'Reilly and E. May, J. Virol. 61, 167-176, 1987). By analysing a series of clustered point mutations generated throughout the enhancer region we mapped domain I from nt 232 to 272 and domain II from nt 184 to 216. These two domains which are required for late promoter activity both in the presence and in the absence of T antigen correspond closely to the domains B and A respectively, identified for enhancer function (M. Zenke, T. Grundström, H. Matthes, M. Wintzerith, C. Schatz, A. Wildeman and P. Chambon, EMBO J., 5, 387-397, 1986). Similarly to the enhancer function the late promoter elements defined by these two domains contain multiple sequence motifs. Moreover there is a striking overlap between the sequence motifs within domain A, active for early enhancer function and those within domain II involved in efficient late transcription.

The two classes of genes for the major potato tuber protein, patatin, are differentially expressed in tubers and roots

The major potato tuber protein, patatin, is a family of 40kd glycoproteins that constitutes forty per cent of the soluble protein in tubers but is generally undetectable in other tissues. Fused rocket immunoelectro-phoresis was used to detect in roots patatin that is immunologically different from tuber patatin. Western blots of SDS-polyacrylamide gels show root patatin to have a different molecular weight distribution than tuber patatin isoforms, but immunoprecipitation of in vitro translation products shows the patatin precursors to be of similar molecular weight in both tissues. This suggests that post-translational processing may differ in tubers and roots. Northern blots show that tuber and root patatin mRNAs are of similar size, but tuber transcripts are about 100-fold more abundant. 5' S1 nuclease and primer extension mapping suggests the class of patatin transcripts expressed in roots (class II transcripts) to be a subset of patatin transcripts expressed in tubers (classes I and II). Class II patatin mRNAs differ from class I transcripts by the presence of a 22 nucleotide insertion just upstream of the initiation codon. These data demonstrate that expression of the patatin multigene family is differentially regulated in tubers and roots.

Transcription map of the African green monkey lymphotropic papovavirus

The S1 endonuclease mapping technique was employed to characterize polyadenylated RNA molecules encoded by the African green monkey lymphotropic papovavirus (LPV) in B-lymphoblastoid cells of human origin infected with the virus. Two groups of stable transcripts of opposite polarities were identified and mapped. By analogy with other papovaviruses, these molecules were designated as "early" and "late" RNAs. The early transcripts include two RNA molecules consisting of a colinear 3' "main body" of about 1.9 kb spliced to 5' "leaders" of 0.26 and 0.60 kb, respectively. These molecules are presumably mRNAs encoding the LPV large T and small t antigens. Shorter, less abundant early RNA molecules have also been detected but have not been mapped. The late RNAs include three molecules, of which two consist of a common leader of 0.22 kb spliced to main bodies of 1.2 and 1.85 kb, respectively. The third late transcript of 2.3 kb is colinear. These late transcripts are presumably mRNAs encoding the LPV capsid proteins. A survey of the LPV DNA sequence published by M. Pawlita, A. Clad, and H. zur Hausen (1985, Virology 143, 196-211) allowed tentative assignment of the termini and splice sites of the various RNAs to nucleotides in the DNA sequence. The LPV transcription map is similar but not entirely analogous to those of polyoma virus and simian virus 40. These distinctions support a previous classification of LPV as a member of a new subgroup of the polyomaviruses.

Nonmuscle and muscle tropomyosin isoforms are expressed from a single gene by alternative RNA splicing and polyadenylation

The molecular basis for the expression of rat embryonic fibroblast tropomyosin 1 and skeletal muscle beta-tropomyosin was determined. cDNA clones encoding these tropomyosin isoforms exhibit complete identity except for two carboxy-proximal regions (amino acids 189 to 213 and 258 to 284) and different 3'-untranslated sequences. The isoform-specific regions delineate the troponin T-binding domains of skeletal muscle tropomyosin. Analysis of genomic clones indicates that there are two separate loci in the rat genome that contain sequences complementary to these mRNAs. One locus is a pseudogene. The other locus contains a single gene made up of 11 exons and spans approximately 10 kilobases. Sequences common to all mRNAs were found in exons 1 through 5 (amino acids 1 to 188) and exons 8 and 9 (amino acids 214 to 257). Exons 6 and 11 are specific for fibroblast mRNA (amino acids 189 to 213 and 258 to 284, respectively), while exons 7 and 10 are specific for skeletal muscle mRNA (amino acids 189 to 213 and 258 to 284, respectively). In addition, exons 10 and 11 each contain the entire 3'-untranslated sequences of the respective mRNAs including the polyadenylation site. Although the gene is also expressed in smooth muscle (stomach, uterus, and vas deferens), only the fibroblast-type splice products can be detected in these tissues. S1 and primer extension analyses indicate that all mRNAs expressed from this gene are transcribed from a single promoter. The promoter was found to contain G-C-rich sequences, a TATA-like sequence TTTTA, no identifiable CCAAT box, and two putative Sp1-binding sites.

The SPS4 gene of Saccharomyces cerevisiae encodes a major sporulation-specific mRNA

The SPS4 gene of Saccharomyces cerevisiae, a sporulation-specific gene identified previously in a differential hybridization screen of a genomic yeast DNA library, has been characterized further. The protein encoded by this gene was inferred from its nucleotide sequence to be 38,600 daltons with an isoelectric pH of 8.2. Consistent with this, two-dimensional polyacrylamide gel electrophoresis of the in vitro translation products of RNA purified by hybridization with the cloned SPS4 DNA indicated that the SPS4 gene product is a 39-kilodalton, basic protein. This protein was found to be identical in size and charge to a major, sporulation-specific protein identified in a two-dimensional polyacrylamide gel electrophoretic comparison of the in vitro translation products of total RNA from sporulating MATa/MAT alpha cells and asporogenous MAT alpha/MAT alpha cells. A MATa/MAT alpha strain homozygous for a partial deletion of the SPS4 gene appeared, however, to be unaffected in its ability to form viable ascospores.

Novel promoter upstream of the human c-myc gene and regulation of c-myc expression in B-cell lymphomas

A new promoter of the human c-myc gene called P0, with multiple RNA start sites, was mapped over 500 bases upstream of the two previously identified promoters, P1 and P2. Sequencing full-length cDNA clones of P0 RNAs revealed two open reading frames upstream of that for the P64c-myc protein. P0 RNA is located on polyribosomes and released by puromycin, indicating that it functions as an mRNA. In vitro translation of RNA synthesized from the cloned cDNAs predicts that P0 transcripts are translated into a novel 12.5-kilodalton protein corresponding to the first open reading frame. The regulation of P0 RNA was studied in the B-cell lymphoma cell line Manca, in which only the translocated c-myc allele lacking exon 1 was thought to be active. However, we found that P0 transcription and the DNase I-hypersensitive site associated with this promoter persist on the untranslocated allele, even though P1/P2 transcription as measured by a nuclear runoff assay was repressed. These results suggest that allelic exclusion of c-myc expression in this B-cell lymphoma is caused by a repression of transcription which is specific to the P1/P2 promoters. We previously reported a block to elongation of transcription near the 3' end of exon 1 in the wild-type c-myc gene, which results in an excess of exon 1 over exon 2 transcription (5a). In contrast, we found that in the Daudi B-cell lymphoma, which retains exon 1 in the active allele, equimolar transcription of exons 1 and 2 occurs. This result suggests a model for the activation of c-myc in B-cell lymphomas.

Bidirectional promoter elements of simian virus 40 are required for efficient replication of the viral DNA

Mutants of simian virus 40 (SV40) lacking parts of the 72- and 21-base-pair repeat regions were made deficient in large T antigen by recombination with dlA 4000, a mutant containing a frameshift deletion near the amino terminus of the T antigen genes. These double mutants were transfected into COS cells, and the amounts of replicated viral DNA were measured at various times thereafter. It was found that deletion of either the 72- or 21-base-pair repeat region did not significantly reduce the accumulation of viral DNA. However, cells transfected with mutants lacking both of these promoter elements accumulated 100-fold less viral DNA than cells transfected with wild-type SV40. This indicates that the 72- and 21-base-pair repeat regions are each sufficient for supplying a function required for efficient replication of SV40 DNA. In addition, the ability of either of these regions to support efficient replication was gradually reduced as the number of promoter elements within each was decreased. Since the 72- and 21-base-pair repeat regions bidirectionally induce transcription, our results indicate that bidirectional promoter elements play a role in the replication of viral DNA. However, fewer of these elements are required for efficient replication than for efficient transcription.

Characterization and mutational analysis of a cluster of three genes expressed preferentially during sporulation of Saccharomyces cerevisiae

A differential hybridization screen of a genomic yeast DNA library previously identified 14 genes of Saccharomyces cerevisiae that are expressed preferentially during sporulation. Three of these sporulation-specific genes, SPS1, SPS2, and SPS3, have been shown to be closely linked. A mutational analysis has demonstrated that expression of the SPS1 gene, but not the SPS2 gene, is essential for the completion of sporulation. A diploid MATa/MAT alpha strain homozygous for a disruption of the SPS1 gene failed to form asci when subjected to sporulation conditions. The 3' end of the transcript encoded by the SPS1 gene was found to map only 185 base pairs from the 5' end of the SPS2 gene. The SPS1-SPS2 intergenic region was shown to contain all of the regulatory sequences necessary for the sporulation-specific activation of the SPS2 gene as assessed by expression of a translational SPS2-lacZ fusion gene present on a replicating, centromere-containing plasmid. The fusion gene was found to be expressed at the same time during sporulation as the chromosomal wild-type SPS2 gene.

Termination-reinitiation occurs in the translation of mammalian cell mRNAs

Many examples of internal translation initiation in eucaryotes have accumulated in recent years. In many cases terminators of upstream reading frames precede the internal initiation site, suggesting that translational reinitiation may be a mechanism for initiation at internal AUGs. To test this idea, a series of recombinants was constructed in the mammalian expression vector pSV2. Each contained a dicistronic transcription unit comprising the coding sequence for mouse dihydrofolate reductase (DHFR) followed by the gene for xanthine-guanine phosphoribosyl transferase (XGPRT) from Escherichia coli. Various versions of this pSV2dhfr-gpt recombinant plasmid altered the location at which the DHFR reading frame was terminated relative to the XGPRT initiation codon and demonstrated that this is a critical factor for the expression of XGPRT activity in transfected Cos-1 cells. Thus, when the DHFR frame terminated upstream or a very short distance downstream of the XGPRT initiator AUG, substantial levels of XGPRT activity were observed. When the DHFR frame terminated 50 nucleotides beyond the XGPRT initiator, activity was reduced about twofold. However, when the DHFR and XGPRT sequences were fused in-frame so that ribosomes which initiated at the DHFR AUG did not terminate until they encountered the XGPRT terminator, production of XGPRT activity was abolished. This dependence of internal translation initiation on the position of terminators of the upstream reading frame is consistent with the hypothesis that mammalian ribosomes are capable of translational reinitiation.

The complete nucleotide sequence of the left very early region of Escherichia coli bacteriophage PRD1 coding for the terminal protein and the DNA polymerase

DNA molecules replicating in a linear form have been found in certain viruses and plasmids of both prokaryotic and eukaryotic origin. Characteristic of this type of molecules are the proteins covalently linked to their 5' ends and inverted terminal nucleotide sequences. The molecules replicate via a protein-priming mechanism, where participants include terminal protein and a specific polymerase. We report here the nucleotide sequence of the left very early region of Escherichia coli bacteriophage PRD1. This region codes for the terminal protein and the phage DNA polymerase. The predicted amino acid sequence of the terminal protein does not share homology with those of other known terminal proteins. The PRD1 DNA polymerase shows four regions of extensive homology to that of Bacillus subtilis phage phi 29. One of these conserved regions is also found in several animal virus DNA polymerases.

Characterization of the simian virus 40 late promoter: relative importance of sequences within the 72-base-pair repeats differs before and after viral DNA replication

We examined sequences involved in the simian virus 40 (SV40) late promoter in vivo, by using quantitative S1 nuclease analysis of a series of deletion mutants within the SV40 regulatory region. These mutants were constructed so as to place the altered promoter region in its normal position relative to the SV40 late genes. The effects of the deletions on late transcriptional activity were analyzed before and after viral DNA replication, by omitting or including SV40 large T antigen. The data show that (i) in the absence of large T antigen, the deletion of the 21-base-pair (bp) repeats results in a fourfold increase in late transcription, and (ii) the sequences within the 72-bp repeats are a component of the SV40 late promoter, acting not only before, but also after viral DNA replication. We identified two domains which contain sequences important for efficient late transcription. Domain I, at the late proximal end of each 72-bp repeat, was found to function before replication and was possibly also involved after replication. The contribution of domain II, at the late distal end of each 72-bp repeat, was much more significant after replication but only of minor importance before replication.

The Drosophila melanogaster actin 5C gene uses two transcription initiation sites and three polyadenylation sites to express multiple mRNA species

At least six mRNAs are made from the Drosophila melanogaster act5C gene. We investigated the structures of these RNAs in detail and determined that they are heterogeneous at both their 5' and 3' ends. At the 5' end there were two nonhomologous leader exons which were alternately spliced to the remainder of the gene. These leader exons mapped to 1.7 and 0.7 kilobases, respectively, upstream of a common splice acceptor site which was eight base pairs 5' to the translation initiator AUG. Exon 1 is 147 bases in length, while exon 2 is 111 bases. A consensus TATA sequence was found roughly 30 base pairs upstream from exon 1, but none was found in the analogous position upstream of exon 2. The transcript length diversity arose principally from the use of three polyadenylation sites. This gave rise to RNA molecules with 3'-untranslated regions of roughly 375, 655, and 945 base pairs. With two start sites and three termination sites, this gene has the potential to produce six different transcripts. All six possible transcripts were present in whole fly mRNA. Transcripts containing the two different leader exons were found in roughly the same relative quantities through development. In contrast, the various 3' ends were differentially represented through development.

Sequences involved in initiation of simian virus 40 late transcription in the absence of T antigen

We analyzed the sequences involved in vivo in the initiation of simian virus 40 (SV40) late transcription occurring in the absence of both SV40 origin sequences and T antigen. The constituent elements of the SV40 late promoters have already been the subject of extensive studies. In vitro studies have resulted in the description of two putative domains of the late promoters. The first domain consists of an 11-base-pair (bp) sequence, 5'-GGTACCTAACC-3', located 25 nucleotides (nt) upstream of the SV40 major late initiation site (MLIS) (J. Brady, M. Radonovich, M. Vodkin, V. Natarajan, M. Thoren, G. Das, J. Janik, and N. P. Salzman, Cell 31:624-633, 1982). The second domain is located within the G-C-rich region (J. Brady, M. Radonovich, M. Thoren, G. Das, and N. P. Salzman, Mol. Cell. Biol. 4:133-141; U. Hansen and P. A. Sharp, EMBO J. 2:2293-2303). Our previous in vivo studies permitted us to define a domain of the late promoter which extends from nt 332 to nt 113 and includes the 72-bp enhancer sequences. Here, by using transfection of the appropriate chimeric plasmids into HeLa cells in conjunction with quantitative S1 nuclease analysis, we analyzed in more detail the sequences required for the control of SV40 late-gene expression occurring before the onset of viral DNA replication. We showed that the major late promoter element is in fact the 72-bp repeat enhancer element. This element was able to drive efficient late transcription in the absence of T antigen. Under our experimental conditions, removal of the G-C-rich region (21-bp repeats) entailed a significant increase in the level of late-gene expression. Moreover, translocation of this element closer to the MLIS (53 nt upstream of the MLIS) enhanced the level of transcripts initiated at natural late initiation sites. Our results suggest that the G-C-rich regions have to be positioned between the enhancer element and the initiation sites to stimulate transcription from downstream sites. Thus, the relative arrangement of the various promoter elements is a critical factor contributing to the situation in which the early promoter is stronger than late promoters before viral DNA replication.

Simian virus 40 agnoprotein facilitates normal nuclear location of the major capsid polypeptide and cell-to-cell spread of virus

The simian virus 40 agnoprotein is a 61-amino-acid, highly basic polypeptide that is coded within the 5' leader of late 16S mRNAs. To better understand agnoprotein function and to more effectively differentiate cis-from trans-acting effects of an agnogene mutation, we constructed a mutant virus that carries a single-base-pair substitution and fails to produce agnoprotein. pm 1493 contains a T/A to A/T transversion at sequence position 335. This mutation converts the agnoprotein initiation codon from ATG to TTG, preventing synthesis of the protein. The mutant displays only a modest growth defect in CV-1P and AGMK cells and no defect in BSC-1 cells. Early-gene expression, DNA replication, synthesis of late viral products, and the kinetics of virion assembly all appear normal in pm 1493-infected CV-1P cells. Immunofluorescent studies, however, indicate that localization of the major capsid polypeptide VP1 is different in mutant- than wild-type virus-infected cells. Furthermore, the lack of agnoprotein led to inefficient release of mature virus from the infected cell. Agnogene mutants could be severely compromised in their ability to propagate in monkeys given their reduced capacity for cell-to-cell spread.

The SPS4 gene of Saccharomyces cerevisiae encodes a major sporulation-specific mRNA

The SPS4 gene of Saccharomyces cerevisiae, a sporulation-specific gene identified previously in a differential hybridization screen of a genomic yeast DNA library, has been characterized further. The protein encoded by this gene was inferred from its nucleotide sequence to be 38,600 daltons with an isoelectric pH of 8.2. Consistent with this, two-dimensional polyacrylamide gel electrophoresis of the in vitro translation products of RNA purified by hybridization with the cloned SPS4 DNA indicated that the SPS4 gene product is a 39-kilodalton, basic protein. This protein was found to be identical in size and charge to a major, sporulation-specific protein identified in a two-dimensional polyacrylamide gel electrophoretic comparison of the in vitro translation products of total RNA from sporulating MATa/MAT alpha cells and asporogenous MAT alpha/MAT alpha cells. A MATa/MAT alpha strain homozygous for a partial deletion of the SPS4 gene appeared, however, to be unaffected in its ability to form viable ascospores.