A novel method to map transcripts: evidence for homology between an adenovirus mRNA and discrete multiple regions of the viral genome

Synthesis of the Ad2+ND5-specified 42K protein is regulated posttranscriptionally in abortively infected monkey cells

In abortive infections of monkey cells by Ad2+ND5, the synthesis of the simian virus 40-specific 42,000-molecular-weight (42K) protein was reduced approximately 10-fold compared with a productive coinfection by Ad2+ND5 plus Ad2hr400 and about 20-fold compared with productive infections by Ad2+ND5 plus simian virus 40 or by Ad2+ND2 alone. However, the level of Ad2+ND5-specific mRNA was depressed twofold or less in abortive infections compared with productive infections. Moreover, the 42K mRNA isolated from abortive Ad2+ND5 infections translated in vitro with the same efficiency as the mRNA isolated from productive coinfections. This is analogous to the block to synthesis of the adenovirus fiber polypeptide in monkey cells (Anderson and Klessig, J. Mol. Appl. Genet. 2:31-43, 1983). Also like fiber protein, the increased level of the 42K protein found in productive infections was due to enhanced synthesis, not increased stability of the protein. Our results suggest that the synthesis of the Ad2+ND5-specified 42K protein and the adenovirus fiber protein are regulated in similar posttranscriptional manners.

DNA sequence of the leftward junction in the adenovirus-simian virus 40 hybrid Ad2+D2 and determination of the structure of the D2-T antigen

The nucleotide sequence of the junction between the simian virus 40 early region and the adenovirus type 2 late region L4 in the hybrid virus Ad2+D2 was determined. The deduced amino acid sequence suggests that the D2-T antigen is a chimeric protein sharing 594 amino acids with the C-terminal end of the simian virus 40 T antigen and 104 amino acids with the N terminus of the adenovirus type 2 33,000-molecular-weight protein. The predicted structure of the D2-T antigen was confirmed by an immunoprecipitation analysis.

The nucleotide sequence at the recombination/integration sites of the hybrid viruses Ad2+ND3 and Ad2+ND5

The nucleotide sequence at the recombination/integration sites of the adenovirus 2-simian virus 40 hybrid viruses, Ad2+ND3 and Ad2+ND5, is reported. These viruses were obtained by passages through human cells and fail to express the SV40-related proteins. The lack of expression of SV40-related proteins has been explained on the basis of the nucleotide sequence at the recombination sites. Ad2+ND3 has the entire reading frame for the SV40 T antigen removed up to the translation termination codon. The recombination event in Ad2+ND5 was found to occur in the leader region 11 nucleotides upstream from the splice junction, thus totally eliminating the naturally occurring splice site, which might have lead to defective processing of the mRNA. Alternatively, because of the large deletion, this virus is incapable of making similar hybrid proteins as in Ad2+ND1, Ad2+ND2, and Ad2+ND4, which share the N-terminal sequence of the 16-kDa glycoprotein of the wild-type virus. Thus, either one or both of these events may explain the lack of synthesis of the SV40 T antigen specific protein. Ad2+ND3 and Ad2+ND5 share the sequences at the right junction which suggests their origin from a common precursor. Also, the recombination was found to result in the disruption of the poly (A) addition signal of the adenovirus 2 early region III transcripts. All of the junction sequences were found to be rich in A:T base pairs.

Mode of proviral activation of a putative mammary oncogene (int-1) on mouse chromosome 15

Most mammary carcinomas induced in C3H mice by the mouse mammary tumour virus (MMTV) bear a new proviral insertion within a highly conserved locus on chromosome 15 called int-1. A transcriptional unit within this locus is inactive in all tested normal tissues but expressed at low levels in mammary tumours with proviral insertions positioned on either the 5' and 3' sides of the gene. Transcription of the proviruses proceeds away from int-1; thus an indirect mechanism appears to activate expression of this putative oncogene.

Translational control of SV40 T antigen expressed from the adenovirus late promoter

We have constructed four novel adenovirus-SV40 hybrid viruses that contain the SV40 A gene at different positions downstream from the adenoviral major late promoter, within the region that encodes the second and third segments of the late tripartite RNA leader. The SV40 insert was precisely positioned in preselected regions of the adenoviral genome by using a combination of in vitro and in vivo recombination. As expected, all four recombinants produce equally high levels of SV40-encoded RNA that initiates at the adenovirus late promoter and contains two or three leader segments at the 5' end. Yet, in spite of this efficient transcription, only one virus, Ad-SVR284, directs the synthesis of high levels of SV40 large T antigen in infected cells; the other recombinants all produce approximately 20-fold less T antigen. This differential expression is, however, not seen in vitro, where equal amounts of hybrid T mRNA direct the synthesis of equal amounts of SV40 T antigen. Thus, some form of translational regulation is present in adenovirus-infected cells that is missing from the in vitro translation reaction.

Expression of rDNA insertions during rDNA magnification in D. melanogaster

In D. melanogaster, many ribosomal genes contain an intervening sequence that interrupts the 28S rRNA gene. In wild-type flies, type I and type II insertions are rarely transcribed and the transcripts of the interrupted genetic units do not contribute significantly to the production of mature ribosomal RNA. We demonstrate that during rDNA magnification, transcription of short type I sequences and of type II sequences is respectively, about 4- and about 16-fold that observed in unmagnified homozygous bobbed females used as control. In subsequent generation (bbm1) we have observed, for transcription of short type I sequences, that this elevated level is maintained and, for transcription of type II sequences, that the level reverts to one comparable with the control. Transcription of both insertion sequences decreases in subsequent generations (bbm19), reaching a level comparable with the controls.

Efficient recovery of functionally intact mRNA from agarose gels via transfer to an ion-exchange membrane

A simple method is described for the efficient recovery of intact mRNA from high resolution agarose gels. Fractionation of RNA is accomplished by gel electrophoresis under denaturing conditions using methylmercuric hydroxide. The RNA in the gel is then transferred electrophoretically to a diethylaminoethyl (DEAE)-membrane. After reversing the methylmercuric modification of the RNA, the membrane is sliced into narrow sections and the RNA is eluted at 65 degrees with a high ionic strength buffer containing 6M guanidine hydrochloride. RNA isolated by this procedure is suitable for subsequent enzymatic reactions, including in vitro translation and reverse transcription. The major advantages offered by this procedure are: 1) The membrane-bound RNA is a replica of the high resolution fractionation pattern achieved in the gel. 2) The immobilization and concentration of RNA and the removal of gel matrix contaminants are all accomplished in one step. 3) Small quantities of RNA are efficiently recovered and are suitable for subsequent biochemical manipulations. The method is of general utility for any biological system. We have applied its use to the fractionation, recovery, and analysis of mRNA from Xenopus liver and have identified cDNA clones complementary to albumin mRNA.

Sandwich hybridization as a convenient method for the detection of nucleic acids in crude samples

A method based on three-DNA-component, sandwich hybridization has been designed for the detection and quantitation of nucleic acids in crude samples using adenovirus DNA as a model. Two non-overlapping restriction fragments of adenovirus type 2 (Ad2) DNA were cloned into two vectors, the pBR322 plasmid and M13 phage. The recombinant plasmid DNA was immobilized onto nitrocellulose filters and the single-stranded recombinant phage DNA was labeled with 125I and used as a probe. When these two reagents were incubated under annealing conditions no radioactivity became filter-bound; only if denatured adenovirus DNA was added as the third reagent, it mediated the attachment of the radioactive probe to the filters. Hybridization efficiency was shown to be dependent on both the filter and probe DNA concentrations and on the hybridization conditions. When standardized, the assay is quantitative, and under the conditions used 0.2 ng of adenovirus DNA (8 X 10(-6) pmol) could be detected by an overnight incubation. The test is suitable for crude samples, e.g., solubilized cell extracts, without any purification steps. Less than 100 cells infected with Ad2 can be detected, implying that the assay could be applicable to virus diagnostics.

The nucleotide sequence of mRNA for the Mr 19 000 glycoprotein from early gene block III of adenovirus 2

The cytoplasmic poly(A)RNA from early stages of infection of HeLa cells by adenovirus 2 (Ad2), was used to synthesize cDNA. The resulting cDNA segments were inserted at the PstI site of the plasmid pBR322 after dG/dC tailing. The clones containing sequences corresponding to early region III transcripts were identified by hybridization against the SmaI-C fragment (76.5 to 91.9 map units) of the Ad2 genome. The clone pE22 which contained a copy of the mRNA coding for the Mr 19 000 glycoprotein was characterized in detail. A comparison with the genomic sequences allowed the identification of the splice between the x and y leaders. The nucleotide sequences CCGGTG and CAGTTT were found at the donor and acceptor sites of the splice junction, respectively. The coding region consisted of a continuous stretch of 159 amino acids with a hydrophobic N-terminus and two possible glycosylation sites. The triplet ATG was encountered twice in phase 3 before the actual site of initiation of translation, which was in phase 2. The 3'-untranslated region was 500 nucleotides long and contained an open, translational reading frame for a Mr 11 000 protein, following a potential initiator ATG. The sequence ATTAAA was observed 17 bp before the poly(A) tail.

Adenovirus type 12-transformed rat embryo brain and rat liver epithelial cell lines: adenovirus type 12 genome content and viral protein expression

By Southern blotting analysis, six adenovirus type 12 (Ad-12)-transformed rat embryo brain cell lines and one Ad-12-transformed rat liver epithelial line were shown to contain all or nearly all the Ad-12 genome. Another Ad-12 rat liver epithelial cell line contained a repeating structure consisting of only the left-hand 16% of the Ad-12 genome. Three Ad-12-specified proteins (molecular weights, 52,000, 41,000, and 18,000) were found by immunoprecipitation to be common to all of these cell lines. Two rat liver epithelial lines, produced from an Ad-12-infected culture and previously shown to be T-antigen negative by immunofluorescence, contained no detectable Ad-12 genome or Ad-12-specified proteins. Although some of the rat embryo brain transformants had been shown previously to express "late" Ad-12 mRNA, no Ad-12 structural proteins were found to be produced by these cell lines.

Multiple arrangements of viral DNA and an activated host oncogene in bursal lymphomas

Proviruses of avian leukosis virus (ALV) are located in the vicinity of a putative cellular oncogene (c-myc) in ALV-induced bursal lymphomas. Enhanced expression of c-myc occurs in association with proviruses found in any of three configurations: (I) on the 5' side ('upstream') of c-myc in the same transcriptional orientation; (II) on the 3' side ('downstream') of c-myc in the same orientation; (III) upstream, in the transcriptional orientation opposite to that of c-myc. Thus, activation of adjacent cellular genes by retroviral DNA can involve mechanisms other than provision of a transcriptional promoter.

Transcription of sea urchin histone genes in Escherichia coli

DNA fragments comprising units of the repeated histone genes form the sea urchins Psammechinus miliaris and Echinus esculentus were placed under the control of bacteriophage Lambda promoters by cloning into lambda replacement vectors. Although promoter-like regions exist within the cloned fragments, transcription of the histone genes is controlled mainly, but not exclusively, by lambda PL promoter. A transcription map of the cloned P. miliaris histone DNA fragment was obtained. The order of histone genes in E. esculentus was deduced from electron microscopic analyses of heteroduplexes with P. miliaris histone genes, and is similar to that in P. miliaris. Translation products of the transcripts have not been found in E. coli.

A possible regulatory mechanism in RNA processing and its implication for posttranscriptional sequence control during differentiation of cell function

1. This paper is concerned with the possible molecular mechanism for RNA processing including posttranscriptional sequence control underlying the differentiation of cell functions. 2. It was previously postulated that intramolecular double-stranded hairpin structures present at 5'- and 3'-terminal regions of a 'pre-mRNA' are key elements for RNA splicing [24]. 3. In this paper the possibility is considered that the splicing of 'pre-mRNA' can be regulated in such a way that the formation of the proper double-stranded hairpin structures is prevented by the binding of low-molecular-weight nuclear RNA (LnRNA) to the terminal regions and/or to the nucleotide sequences around the exon-intron and intron-exon joint sites of the 'pre-mRNA' molecules. 4. Complementarity assessment of nucleotide sequences of rat preproinsulin 'pre-mRNA' and rat LnRNA, i.e. Ul, showed that Ul RNA is capable of forming stable double-standard intermolecular structures around the joint sites of preproinsulin 'pre-mRNA' and may prevent the formation of intramolecular double-stranded structures required for RNA splicing. This may imply a regulatory (inhibitory) role for Ul RNA in the processing of 'pre-mRNA'. 5. A possible regulatory role of LnRNA in RNA splicing is discussed in relation to the determination of the mRNA population to be translated in the cytoplasm during differentiation of cell functions.

Expression of early genes of origin-defective mutants of simian virus 40

The nucleotide sequences of eight origin-defective mutants of simian virus 40 have been determined. All of the mutants have suffered deletions, which range in size from 4 to 241 nucleotides. Some of the mutants induce the synthesis of tumor (T) antigen, others do not. Viral mRNA extracted from rat cells transformed by two of the T-antigen-positive mutants has been analyzed by the S1 nuclease technique of Berk and Sharp. Irrespective of the size or the location of the deletions, the 5' ends of viral mRNAs are located approximately the same distance from the A+T-rich region (A-T-T-T-A-T) rather than at a specific site in the viral genome.

Splicing of the late mRNAs of polyoma virus does not occur in the cytoplasm of the infected cell

The three mRNAs that encode the capsid proteins of polyoma virus are produced by the excision of different sequences from continuous transcripts of the L strand of viral DNA. All three of the mRNAs have long half lives, and the larger species are not converted to the smaller ones to any measurable extent within the cytoplasm. Therefore the cytoplasmic proportions of late polyoma mRNAs are predetermined by splicing that is confined to the nucleus of the infected cell and which is complete by the time that mRNA is transported to the cytoplasm.

Expression of ribosomal DNA insertions in Drosophila melanogaster

Approximately half of the ribosomal genes on the X chromosome of Drosophila melanogaster are interrupted by an insertion of type 1. Nuclear RNA from D. melanogaster embryos was transferred to DBM paper and hybridized with cloned type 1 insertion sequences. With a DNA fragment derived specifically from large insertions, transcripts were detected between 5 and 10 kb. These insertion transcripts represent less than one RNA molecule per nucleus, which is more than three orders of magnitude below the concentration of nascent rRNA chains, as determined by kinetics of hybridization. With a DNA fragment derived from the right end of large insertions which is also complementary to short insertions, more discrete RNA bands appeared with sizes between 1 and 8.5 kb, representing altogether about 13 RNA molecules per nucleus. Insertion transcripts large enough to be potential precursors to 28S rRNA represent less than one molecule per nucleus. It was shown by sandwich hybridization that at least some of the insertion transcripts are derived from rDNA. No significant difference was found between insertion transcripts in RNA extracted from ovaries, embryos, larvae, pupae or adult flies. Unless a mechanism other than splicing is involved, ribosomal genes with insertions cannot contribute significantly to the synthesis of 28S rRNA. A cytoplasmic RNA approximately 1 kb long, which is complementary to a short insertion and to ribosomal gene sequences flanking both sides of the insertion, was found. The abundance of this short unspliced RNA is about 50 molecules per embryo cell.

The intervening sequence in the 26S rRNA coding region of T. thermophila is transcribed within the largest stable precursor for rRNA

We studied the transcription of the intervening sequence in the 26S rRNA coding region of the extrachromosomal rDNA molecules in the macronucleus of T. thermophila by hybridization of purified nuclear rRNA precursors or cytoplasmic 26S rRNA to purified native rDNA or specific rDNA restriction fragments. Examination of R loop hybrids in the electron microscope and analyses of S1-protected rDNA fragments in alkaline agarose gels showed that mature 26S rRNA, nuclear pre-26S rRNA and a fraction of the pre-rRNA molecules containing both the sequences for 17S and 26S rRNA all lack the region corresponding to the intervening sequence. The rest of the pre-rRNA molecules, however, hybridize in a colinear fashion to the whole coding region, and thus must contain the intervening sequence. We can conclude from these results that the intervening sequence is transcribed within the primary transcription product of the rDNA, and that the post-transcriptional removal of the intervening RNA sequence is a very early processing event in the organism.

Transcription maps of mtDNAs of two strains of saccharomyces: transcription of strain-specific insertions; Complex RNA maturation and splicing

We have developed a two-dimensional method for simultaneously mapping on the yeast mtDNA genome all the transcripts representing more than 0.01% of mtRNA. In two yeast strains, Saccharomyces carlsbergensis NCYC-74 and Saccharomyces cerevisiae KL14-4A, about 25 discrete transcripts were found apart from tRNAs. The mtDNAs of these strains differ by the absence (NCYC-74) or presence (KL 14-4A) of various large insertions located within genetically active regions. The transcripts can all be related to known loci on the genetic map. In nearly all cases the RNAs are much longer than required to specify the known protein product of the locus concerned. The organization of the transcripts is similar in the two strains except at the positions of the large insertions (500-3300 bp) in the oxi-3 and cob loci. The sequences of these insertions are present in RNA species larger than 25S, but are absent from smaller transcripts of the same regions. This is probably due to splicing, since the coding sequences for most of these smaller transcripts are noncontiguous. The smaller transcripts of other loci also seem to arise from processing of larger RNA species. The oxi-3 locus, containing the structural gene for cytochrome c oxidase subunit l, is transcribed in a very complex fashion that suggests differential splicing into partially overlapping transcripts. This may indicate that oxi-3 has additional genetic functions, including possible control of the biosynthesis of cytochrome c oxidase holoenzyme or its assembly into the mitochondrial inner membrane. As in the case of the eucaryote nucleus, the regulation of mitochondrial gene expression seems to occur more at the level of RNA processing than has been recognized thus far.

Sequence analysis of adenovirus DNA: complete nucleotide sequence of the spliced 5' noncoding region of adenovirus 2 hexon messenger RNA

The complete nucleotide sequence of the 5' noncoding region of the adenovirus 2 hexon messenger RNA has been established by sequence analysis of reverse transcripts. Such transcripts were generated by extension of specific single-stranded DNA primers with reverse transcriptase after hybridization to purified hexon mRNA. The total length of the 5' noncoding region was determined to be 240 nucleotides, of which the spliced tripartite leader sequence contributes 202 nucleotides including the terminal m7G. The sizes of the different segments of the tripartite leader were estimated by comparing the established mRNA sequence with the genomic sequences for the first and third leader segments, and were found to be 42 nucleotides for the first segment, 71 nucleotides for the second and 89 nucleotides for the third. The estimates are ambiguous, however, due to the presence of tandemly repeated sequences at both ends of the intervening sequence between the third leader segment and the body of the hexon mRNA. The sequence of the leader allows the formation of hydrogen-bonded interactions with the 3' end of 18S ribosomal RNA near the capped 5' end and also close to the initiator AUG.

Nucleotide sequence analysis of the leader segments in a cloned copy of adenovirus 2 fiber mRNA

Fiber mRNA of adenovirus 2 has been used as a template for RNA-dependent DNA polymerase. The resulting cDNA/RNA hybrids have been inserted at the Pst I site of the plasmid vector pBR322 after A:T tailing. One recombinant plasmid, pJAW 43, has been characterized in detail and shown to contain sequences from the main body of fiber mRNA, the three leaders common to most late adenoviral mRNAs and a fourth leader found in some species of fiber mRNA. The complete DNA sequence of the leader region has been determined and does not contain the initiation codon AUG, although this codon does occur immediately downstream from the junction between the fourth leader and the main body of the fiber mRNA. The first leader (map coordinate 16.6) is 41 nucleotides long, the second (from 19.6) is 71 nucleotides, the third (from 26.6) is 88 nucleotides and the fourth (from 78.5) is 181 nucleotides. The location of junctions between viral leaders and intervening sequences has been determined by reference, where possible, to sequences of the adenovirus 2 genome. Although the presence of short repeated sequences at the boundaries of intervening sequences and leaders makes it impossible to locate the splice point unambiguously, all of the leader-intervening sequence junctions can be arranged to stress a common feature--the presence of the dinucleotides GT and AG at the 5' and 3' ends, respectively, of the intervening sequences. This prototype sequence, which has also been recognized at or near the splice points in other eucaryotic systems, is possibly part of a larger unit which serves as a recognition site for specific excision-ligation events that ultimately lead to the production of mature mRNAs.

An intervening sequence in the gene coding for 25S ribosomal RNA of Tetrahymena pigmentosa

An intervening sequence of approximately 400 bp has been discovered in the 25S ribosomal RNA gene (rDNA) from macronuclei of Tetrahymena pigmentosa strain 6UM. Another strain, 8ALP, lacks the intervening sequence in its macronuclear rDNA. The presence of the intervening sequence was first suggested by a comparison of the restriction endonuclease maps of the rDNA from each strain. A region which differed in size between the two strains was shown to lie within the region coding for 25S ribosomal RNA by hybridization of the restriction fragments to labeled 25S rRNA. Direct visual evidence for the existence of the intervening sequence in 6UM and its absence from 8ALP was obtained by electron microscopy of R loop hybrids formed between the rDNA and 25S rRNA. The size and position of the intervening sequence within the gene were further defined by detailed restriction analyses of cloned fragments of the rDNA from each strain. The rDNA within the macronucleus of each of these strains is homogeneous, and thus the intervening sequence in the rDNA of strain 6UM must not interfere with transcription of the gene. Furthermore, the presence or absence of the intervening sequence has no obvious functional importance, since both strains can survive and grow equally well.

Amplification in the leader sequence of late polyoma virus mRNAs

Ribonuclease T1 fingerprints of the three "late" polyoma virus mRNAs show that oligonucleotides of the leader sequence are present in multiple copies in each mRNA. These oligonucleotides, however, appear unimolar in fingerprints of complete, continuous transcripts of the late strand of the viral DNA. Oligonucleotides which are represented only once in the DNA are thus reiterated in the mature mRNAs. Consequently, when mRNA was hybridized to the leader region of immobilized viral DNA, those copies present in excess of their genomic representation failed to hybridize and were released by RNAase treatment. Analysis of the RNAase-resistant hybrids revealed a series of leader species with complex sequence arrangements. We suggest that these complicated reiterated sequences are generated during the processing of a precursor RNA which extends several times around the genome. This RNA would be shortened by a series of splicing reactions which conserve sequences from the leader region and attach them to a suitable coding sequence.

The nucleotide sequence of the transforming HpaI-E fragment of adenovirus type 5 DNA

The primary structure of the HpaI-E fragment of adenovirus type 5 (Ad5) DNA has been determined, mainly by the method of Maxam and Gilbert (1977). This fragment comprises the leftmost 4.5% of the Ad5 genome, and has been shown to be the shortest DNA fragment capable of transforming cells. The identification of potential initiation and termination codons in the determined sequence indicates that two small polypeptides consisting of 186, and 81 amino acids, respectively, could be synthesized. Taking into account recent data on RNA splicing, a possibility is considered that this DNA may code also for larger polypeptides.

Proteins bound to heterogeneous nuclear RNA of simian-virus-40-infected cells

Heterogeneous nuclear RNA . protein (hnRNA . protein) complexes from simian-virus-40 (SV40)-infected cells late in infection contain 7--10% RNA sequences specific to SV40 DNA. The SV40 nuclear RNA . protein complexes sediment at 60--70 S. The reality and specificity of the RNA-protein association is shown in metrizamide gradients. Protein and RNA lebels of hnRNA . protein-particles in SV40-infected cells follow a parallel pattern with a peak at 1.28 g/cm2 whereas a mixture of ribosomal RNA and soluble cytoplasmic proteins is separated according to the different densities in metrizamide. Analysis of hnRNA . protein from infected cells by two-dimensional gel electrophoresis shows the presence of a number of new proteins. It is demonstrated that three of these proteins are cellular ones induced by the virus infection and hence constitute good candidates to be specific RNA . protein particles for virus nuclear RNA. The presence of actin in hnRNA . protein particles from normal and SV40-infected cells and the presence of the major capsid protein VP1 in hnRNA . protein particles from SV40-infected cells is discussed.

Comparison of cloned rabbit and mouse beta-globin genes showing strong evolutionary divergence of two homologous pairs of introns

Cloned beta-globin genes of both mouse and rabbit each contain a large and a small intervening sequence (intron) of about equal length at precisely the same positions relative to the coding sequence. The homologous introns show some sequence similarity, particularly at the junctions with the coding sequence. They most probably arose from a common ancestral sequence and diverged substantially during evolution.

The spliced structures of adenovirus 2 fiber message and the other late mRNAs

All late adenovirus 2 messenger RNAs, except perhaps that for peptide IX, are composite molecules with sequences derived from at least two to five or more separate portions of the genome, as determined by electron microscopic analyses of polysomal RNA hybridized to single- or double-stranded DNA. We previously reported that eight different rightward-transcribed mRNAs contain, at their 5' ends, a common three-part leader sequence derived from coordinates 16.6, 19.6 and 26.6, and that a ninth mRNA consists of sequences from 4.6--6.1 linked directly to those from 9.7--11.0 (Chow et al., 1977a; revised coordinates). We now demonstrate that four additional RNA species also have the same tripartite leader joined to messages with 5' ends located at coordinates at 29.1, 30.5, 33.9 and 42.8. The RNA transcript extending from 29.1--39.0 covers most or all of the viral associated (VA) RNA genes (29.0--30.1). The late RNAs can be grouped into several families of transcripts in which two or three mRNAs have the same 3' end and 3' proximal sequences, but differ substantially in length at the 5' end and, therefore, the coordinate at which the leader sequences are attached to the main body of the message. The number of RNA species transcribed from the Ad2 chromosome between coordinates 29 and 50 exceeds the number of identified Ad2 proteins. Several pairs of messages differing in length by a few percent may thus encode the same protein or have a precursor-product relationship. We have also found that a subpopulation of the polysomal mRNAs for the fiber protein, the most distal gene (86.3--91.2) in the rightward transcription unit, has a fourth leader component "y" (78.6--79.1) in addition to the common tripartite leader sequences. Less frequent fiber RNA species have fifth "x" (76.9--77.3) and/or sixth "z" (84.7--85.1) leader segments. Transcripts with x, y or z segments might be processing intermediates, and it is possible to arrange these species into an array suggestive of multiple pathways for the maturation of fiber mRNA. mRNA transcribed at late times from the L strand between coordinates 15.0 and 11.0 has a single component leader located 200 bases from the main body of the gene from coordinate 16.1 to 15.7. This leader originates from a site very close to the first leader component (16.5--16.6) of the R strand messages and suggests the presence of adjacent L and R strand promoters from which transcription diverges. Taken together, these results emphasize the diversity of splicing patterns and the variety of recombined sequences generated during the synthesis of late Ad2 mRNAs.

Biochemical studies on bovine adenovirus type 3. III. Cleavage maps of viral DNA by restriction endoncleases EcoRI, BamHI, and HindIII

Cleavage of bovine adenovirus type 3 (BAV3) DNA by restriction endonucleases EcoRI, BamHI, and HindIII yielded 7 (A to G), 5 (A to E), and 12 (A to L) fragments, respectively. The order of these fragments has been determined to be GDACBFE for EcoRI fragments, AEBDC for BamHI fragments, and JEBKACDHFGIL for HindIII fragments, and cleavage sites of these enzymes have been mapped on the genome of BAV3. BAV3 preparation contains incomplete virus whose genome has a deletion of about 13% of complete virus genome. Restriction endonuclease digestion of the incomplete virus DNA revealed that EcoRI E and F, BamHI C and HindIII G, I, and L fragments were deleted. Therefore, the deleted region of incomplete virus DNA is located near the right-hand end of the BAV3 DNA molecule, a result consistent with our previous electron-microscopic observations on heteroduplex molecules formed between complete and incomplete BAV3 DNA.