Nucleotide sequence and genetic organization of the polyoma late region: Features common to the polyoma early region and SV40

Deininger, Prescott L.; Esty, A; LaPorte, Patricia; Friedmann, Theodore

doi:10.1016/0092-8674(79)90130-2

Cited by 53 publications

(38 citation statements)

References 26 publications

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“…Kamen and co-workers (10,28) have shown that transcription initiates at multiple sites over a 100-nucleotide region between nucleotides 5050 and 5150 in the A2 strain of polyomavirus. Heiser and Eckhart (16) found essentially identical results for the A3 strain, whose DNA sequence does not significantly differ from the A2 strain in this region (11,25,29). Our strain of polyomavirus, which we call AT3, is closely related to strain A3 but contains a 75-nucleotide direct repeat inserted immediately to the left of nucleotide 5175 ( Fig.…”

Section: Methodssupporting

confidence: 50%

Use of a novel S1 nuclease RNA-mapping technique to measure efficiency of transcription termination on polyomavirus DNA.

Tseng¹,

Acheson²

1986

Mol. Cell. Biol.

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We devised a strategy to measure the efficiency of transcription termination in vivo by RNA polymerase on polyomavirus DNA. Pulse-labeled nuclear RNA was hybridized with a single-stranded polyomavirus DNA fragment which spans the transcription initiation region. Hybrids were treated with RNase, bound to nitrocellulose filters, eluted with S1 nuclease, and analyzed by gel electrophoresis. The ratio of full-length to less-than-full-length DNA-RNA hybrids was used to calculate transcription termination frequency. We found that 50% of the polymerases terminated per traverse of the L DNA strand during the late phase of infection. The method for mapping in vivo pulse-labeled RNAs which we developed is potentially useful for studying unstable cellular or viral RNAs.RNA polymerase II does not efficiently terminate transcription on the L strand of polyomavirus DNA during the late phase of productive infection (1). As a result, some RNA polymerase molecules traverse the circular, 5.3-kilobase (kb), double-stranded polyomavirus genome several times before dissociating and releasing their RNA chains. RNA molecules up to four times genome length have been detected in the nuclei of productively infected cells (4,5). These multigenome-length RNAs undergo splicing within the nucleus to form 19S, 18S, and 16S viral mRNAs (18,27).

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Section: Methodssupporting

confidence: 50%

Use of a novel S1 nuclease RNA-mapping technique to measure efficiency of transcription termination on polyomavirus DNA.

Tseng¹,

Acheson²

1986

Mol. Cell. Biol.

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“…7 were eluted and subjected to secondary analysis with pancreatic RNase. The compositions of these oligonucleotides were then compared with the catalog of all T, oligonucleotides predicted by the known DNA sequence of the genome (11,15,39). This analysis confirmed many of the identities indicated by visual comparisons of the fingerprints and verified the conclusion that the apparently missing spots derive from RNA sequences not represented in the mature mRNA's.…”

Section: Resultsmentioning

confidence: 56%

“…We chose the polyoma virus late transcript for several reasons. Not only has the polyoma virus genome been completely sequenced, but its expression in the form ofnuclear transcripts, cytoplasmic mRNA's, and proteins is well understood (11,15,39). The late region of the viral deoxyribonucleic acid (DNA), corresponding approximately to the bottom half of the 5.29-kilobase circular genome (Fig.…”

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confidence: 99%

Arrangement of 30S heterogeneous nuclear ribonucleoprotein on polyoma virus late nuclear transcripts.

Steitz

Kamen

1981

Mol. Cell. Biol.

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Heterogeneous nuclear ribonucleic acid (hnRNA) molecules in eucaryotic cell nuclei associate with a well-defined group of abundant, highly conserved proteins to form heterogeneous nuclear ribonucleoproteins (hnRNP). The exact manner in which these 30S complexes assemble on nuclear transcripts, however, has not been well documented. To determine whether any site selectivity in the formation of hnRNP can be detected (e.g., preferential recognition of intervening sequences or of premessage regions), we investigated the distribution of 30S hnRNP on a particular nuclear RNA, the polyoma virus late transcript. Hybridization studies showed not only that the majority of polyoma late nuclear RNA sequences can be isolated in the form of 30S complexes, but that the RNP were located equally on intervening sequences and premessage portions of the transcript. The latter conclusion was confirmed by ribonuclease T, oligonucleotide fingerprint analysis of polyoma virus-specific RNA recovered from native 30S complexes. However, fingerprint analysis of the small segments of viral RNA in the 30S fraction that survived extensive ribonuclease treatment revealed that oligonucleotides corresponding to intervening sequences were preferentially lost. We discuss these fmdings in relation to the structure of 30S hnRNP and their function in RNA biogenesis.The nascent transcripts of eucaryotic cells become rapidly associated with protein and appear, in the electron microscope, as beaded structures consisting of globular units several hundred Angstroms in diameter connected by ribonuclease (RNase)-sensitive strands. Superb examples of such micrographs were recently published by McKnight and Miller (29) and Lamb and Daneholt (22). Most of the rapidly labeled ribonucleic acid (RNA) (heterogeneous nuclear RNA [hnRNA]) in mammalian or avian cell nuclei can, moreover, be isolated in the form of RNA-protein complexes sedimenting at about 30S (5,19,25,37). If special care is taken to avoid RNase action during preparation, polyparticdes ranging in size up to 200S can be obtained.The basic 30S heterogeneous nuclear ribonucleoprotein (hnRNP) unit contains 2 x 105 daltons of RNA (about 600 nucleotides) and about threefold as much protein. There are approximately six major or "core" protein components with molecular weights of 30,000 to 40,000. These are prominent nuclear proteins, constituting about 10% of the nonchromatin protein in actively growing cells (19). The six polypeptides, moreover, are highly conserved among higher eucaryotic species in both size and amino acid t Permanent address:

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“…Other overlapping genes in bacteriophages OX174 and G4 are transcribed from independent promoters and then translated in different reading frames, yielding essentially unrelated products from the same coding sequence (4,5). Animal viruses such as polyoma virus and simian virus 40 utilize messenger RNA splicing to synthesize several proteins, either in the same or different reading frames, from one coding sequence (6,7).…”

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confidence: 99%

Overlapping genes at the cheA locus of Escherichia coli.

Smith¹,

Parkinson²

1980

Proc. Natl. Acad. Sci. U.S.A.

154

112

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The cheA locus of Escherichia coli, which is required for chemotactic behavior, encodes two polep tide products designated p[cheA]L and pjcheA]s. The mode of synthesis of these two proteins was investigated b transferring various missense and nonsense mutations to a A transducing phage and observing the mutant cheA products made after infection of ultraviolet-irradiated host cells. Missense mutations had no effect on either the size or the relative amounts of the two cheA polypeptides. Overlapping genes, which synthesize more than one polypeptide product from the same coding sequence, have been observed in a number of bacterial and animal viruses. Some overlapping gene pairs in bacteriophage-for example, A and A* in 4X174 or C and Nu3 in X-are transcribed from a common promoter and translated in the same reading frame, but from different initiation sites, yielding two related proteins (1, 2). The A1 and coat proteins of phage QB are also translated in the same phase but differ at their carboxyl ends due to an inefficient translation termination signal (3). Other overlapping genes in bacteriophages OX174 and G4 are transcribed from independent promoters and then translated in different reading frames, yielding essentially unrelated products from the same coding sequence (4,5). Animal viruses such as polyoma virus and simian virus 40 utilize messenger RNA splicing to synthesize several proteins, either in the same or different reading frames, from one coding sequence (6, 7).Regardless of their mechanism of expression, overlapping genes are generally thought to have evolved as a means of increasing the coding capacity of viral genomes without a concomitant increase in overall genorne size, which in most viruses is limited by the capacity of the virion. According to this view, the evolutionary constraints that accompany the use of the same nucleotide sequence by two different genes are offset by selective pressures to retain a particular genome size. If this were the only factor favoring the existence of overlapping genes, it seems unlikely they would have arisen in bacteria or higher cells, in which limitations on the amount of genetic material are much less severe than in viruses.In this report we describe an apparent case of overlapping genes at the cheA locus in Escherichia colh. Mutants defective in cheA function are viable but nonchemotactib due to an inability to change directions as they swim (8, 9). Silverman, Simon, and coworkers (10, 11) constructed X phages carrying the cheA region and showed that cheA complementation activity was associated with the presence of two polypeptides.t In order to determine the nature of the relationship between these two cheA products, we examined the functional properties and the polypeptide products of a variety of cheA mutants. Our findings are consistent with a model in which both polypeptides are translated independently from the same coding sequence and in the same reading frame, but from different initiation sites. Moreover, each polypeptide may have a distin...

show abstract

Nucleotide sequence and genetic organization of the polyoma late region: Features common to the polyoma early region and SV40

Cited by 53 publications

References 26 publications

Use of a novel S1 nuclease RNA-mapping technique to measure efficiency of transcription termination on polyomavirus DNA.

Use of a novel S1 nuclease RNA-mapping technique to measure efficiency of transcription termination on polyomavirus DNA.

Arrangement of 30S heterogeneous nuclear ribonucleoprotein on polyoma virus late nuclear transcripts.

Overlapping genes at the cheA locus of Escherichia coli.

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