The location of the genes coding for hexon and fiber proteins in adenovirus DNA

Molecular evolution of human species D adenoviruses

Adenoviruses are medium-sized double stranded DNA viruses that infect vertebrates. Human adenoviruses cause an array of diseases. Currently there are 56 human adenovirus types recognized and characterized within seven species (A-G). Of those types, a majority belongs to species D. In this review, the genomic conservation and diversity are examined among human adenoviruses within species D, particularly in contrast to other human adenovirus species. Specifically, homologous recombination is presented as a driving force for the molecular evolution of human adenoviruses and the emergence of new adenovirus pathogens.

The revolution in viral genomics as exemplified by the bioinformatic analysis of human adenoviruses

Over the past 30 years, genomic and bioinformatic analysis of human adenoviruses has been achieved using a variety of DNA sequencing methods; initially with the use of restriction enzymes and more currently with the use of the GS FLX pyrosequencing technology. Following the conception of DNA sequencing in the 1970s, analysis of adenoviruses has evolved from 100 base pair mRNA fragments to entire genomes. Comparative genomics of adenoviruses made its debut in 1984 when nucleotides and amino acids of coding sequences within the hexon genes of two human adenoviruses (HAdV), HAdV-C2 and HAdV-C5, were compared and analyzed. It was determined that there were three different zones (1-393, 394-1410, 1411-2910) within the hexon gene, of which HAdV-C2 and HAdV-C5 shared zones 1 and 3 with 95% and 89.5% nucleotide identity, respectively. In 1992, HAdV-C5 became the first adenovirus genome to be fully sequenced using the Sanger method. Over the next seven years, whole genome analysis and characterization was completed using bioinformatic tools such as blastn, tblastx, ClustalV and FASTA, in order to determine key proteins in species HAdV-A through HAdV-F. The bioinformatic revolution was initiated with the introduction of a novel species, HAdV-G, that was typed and named by the use of whole genome sequencing and phylogenetics as opposed to traditional serology. HAdV bioinformatics will continue to advance as the latest sequencing technology enables scientists to add to and expand the resource databases. As a result of these advancements, how novel HAdVs are typed has changed. Bioinformatic analysis has become the revolutionary tool that has significantly accelerated the in-depth study of HAdV microevolution through comparative genomics.

Evidence of frequent recombination among human adenoviruses

Genome stability is a prerequisite for the production and use of adenoviruses for therapy of genetic diseases and cancer. To test the premise that the adenoviral genome is stable, the phylogenetic relationships of 16 adenovirus C (AdC) field isolates were studied in four genome regions: hexon, fiber, polymerase and E1A. The phylogenetic relationships in the fiber gene concurred with those in the hexon region. In contrast, the non-structural regions had marks of frequent recombination, to the point that an isolate of one serotype could contain non-structural proteins that were identical to the genes from a different serotype. Our results suggest that recombination among circulating adenoviruses is very frequent and plays an important role in shaping the phylogenetic relationships of adenovirus genomes. Analysis of the available complete genome sequences of AdB, AdC and AdD species showed that recombination shuffles genome fragments within a species, but not between species. One of the AdC field isolates possessed the fiber gene of AdC type 6, but a hexon gene that was distinct from all AdC serotypes. This strain could not be typed unambiguously in a neutralization test and might represent a novel serotype of AdC. Comparison of the right end (nt 18838–33452) of this isolate with that of the ATCC Ad6 strain showed clear evidence of multiple recombination events.

The hexon genes of adenoviruses of subgenus C: comparison of the variable regions

We report on a 1402-base pair long DNA sequence, encoding for the variable region and parts of the flanking conserved regions of the human adenovirus type 1 (AV1) hexon, and a DNA sequence comprising 1396 base pairs, encoding for the corresponding regions of the human adenovirus type 6 (AV6) hexon. AV1 and AV6, together with AV2 and AV5, belong to subgenus C. Comparison of the predicted amino acid sequences of AV1 and AV6 with those of AV2 and AV5 revealed that the variable hexon region could be subdivided into highly variable, variable and conserved regions. Regions differing between AV2, AV5, AV1 and AV6 were the same as those which were registered as different when comparing AV40 and AV41 (subgenus F), suggesting that these areas of the hexon protein represent type-specific antigenic determinants. Alignment of the amino acid sequences to the known 3-dimensional structure of the AV2 hexon demonstrated that the major amino acid changes were located in the L1 and L2 loops that form the surface of the hexon. Comparison of sequencing data between the serotypes might elucidate questions concerning evolution within subgenus C.

Recombination in adenovirus: analysis of crossover sites in intertypic overlap recombinants

Overlap recombination has been used as a means of generating intertypic recombinants with crossover sites located within a defined region of the adenovirus genome. Using terminal DNA fragments of adenovirus type 2 and type 5 that overlap within the vicinity of the hexon coding region (51.6-59.7 map units), two different crosses could be studied; in one the overlap entirely encompasses the hexon and there are homologous regions at either side of the overlap where recombination is expected, and in the other only one side of the overlap is capable of sustaining recombination. The overall distribution of crossover sites within the overlap has been determined by restriction endonuclease mapping, and analysed in terms of the extent of homology between Ad2 and Ad5 in this region as defined by the DNA sequences (R. Kinloch, N. Mackay, and V. Mautner (1984). J. Biol. Chem., 259, 6431-6436; G. Akusjärvi, P. Aleström, M. Pettersson, M. Lager, H. Jörnvall, and U. Pettersson (1984). Submitted). Crossovers are found only in regions of relatively high DNA homology, as previously shown for intertypic recombination between temperature-sensitive viruses (M. E. G. Boursnell and V. Mautner (1981). Virology 112, 198-209). The presence of a free DNA end within the heterologous zone is insufficient to overcome the barrier to recombination. In crosses where recombination is confined to a relatively small homologous zone (45.9-53.0 mu) there is no special distribution of crossovers within the interval; no "hot spot" is discernible at the free DNA end, suggesting that a free DNA end is not especially recombinogenic, nor at the junction between the homologous and heterologous zones, suggesting that branch migration up to the heterology does not always occur. A cross designed to furnish evidence for gene conversion gave rise to a "conventional" recombinant with a crossover located within a 21-nucleotide tract of homology.

Recombination in adenovirus: DNA sequence analysis of crossover sites in intertypic recombinants

The nucleotide sequence of the adenovirus type 5 genome has been determined for a 620-bp region that spans the C terminus of the pVI gene and the N terminus of the hexon gene, and compared to the adenovirus type 2 DNA sequence: 25 base changes have been identified, most of which do not lead to alterations in the amino acid sequence and regulatory signals in the region. Crossover sites in three intertypic recombinants have been previously located in this region of the genome by fine restriction mapping. A sequence determination for the three recombinants, and the four ts mutants used in generating the ts+ recombinants, was carried out. The crossovers were in each case located in a small region of complete sequence homology (from 45 to 156 nucleotides long) flanked on either side by sequences derived from each parent. These structures are compatible with a reciprocal crossing over model of generalised recombination, where a recombinant joint has resolved in a region of high DNA homology. For the recombinants considered here, this region abutts onto a neighbouring region of much lower sequence homology, and it is possible that the position of the crossover is determined at least in part by the termination of branch migration at a heterologous boundary.

Analysis of Ad5 hexon and 100K ts mutants using conformation-specific monoclonal antibodies

Adenovirus type 5 ts mutants deficient in hexon metabolism were investigated using conformation-specific monoclonal antibodies directed against hexon capsomeres and the viral 100K protein. The ts mutants map either in the hexon structural gene or in the gene encoding the 100K protein, a major, late nonstructural protein. All of the mutants examined (ts1, ts2, ts3, ts4, ts17, and ts20 of J. F. Williams, M. Gharpure, S. Ustacelebi, and S. McDonald (1971). J. Gen. Virol. 11, 95-101) were unable to produce the capsomeric form of hexon (a trimer of three hexon monomers) at the nonpermissive temperature. However, all of the mutants retained the ability to produce a complex of 100K and hexon which has been demonstrated to play a major role in the assembly of hexon trimers. The mutants accumulated nontrimerized hexon in this ts complex in the perinuclear region of the cell. Several of the mutants (ts1, ts2, ts3) were found to successfully assemble hexon synthesized at the nonpermissive temperature upon shift down to the permissive temperature, even in the presence of a protein synthesis inhibitor. The mutant, ts2, which maps in the hexon structural gene, was found to be dependent on protein synthesis for transport of hexon trimers into the nucleus during temperature shift down, while the 100K ts mutants, ts1 and ts3, were independent of protein synthesis for both hexon assembly and transport.

In vitro construction of a recombinant adenovirus Ad2:Ad5

A hybrid virus containing the left half of the Ad5 genome and the right half of the Ad2 genome has been constructed by ligating together in vitro the BamHI-A fragment of Ad5 (map co-ordinates 0-59.5) to the BamHI-A fragment of Ad2 (map co-ordinates 59.5-100), and using this DNA to transfect susceptible cells. Viable progeny virus has been obtained which grows as well as the parental virus without any requirement for helper virus, and probably contains a hybrid hexon polypeptide consisting of the major part of the Ad5 hexon with an Ad2 carboxy terminus.

Hind III restriction site map of the human adenovirus type 1 DNA

The physical map of human adenovirus type 1 DNA was constructed with the Hind III restriction enzyme. Direct comparison of the DNA fragments with those of adenovirus type 2 revealed that the genome of adenovirus type 1 is 200 to 300 base pairs longer. The difference are located outside the region of the inverted terminal repetition within three distinct loci. Fragment Hind III-F of type 1 DNA which is presumed to carry all the genes responsible for in vitro transformation can be separated without considerable contamination by a single electrophoretic step.

Restriction Map of Rachiplusia ou and Rachiplusia ou-Autographa californica Baculovirus Recombinants

The restriction sites of Rachiplusia ou nuclear polyhedrosis virus (Ro M NPV) DNA were mapped for the endonucleases Sma I, Kpn I, Bam HI, Sac I, Xho I, and Eco RI. Of the 60 DNA restriction sites of Ro M NPV, 35 mapped in similar positions as compared to the restriction sites of Autographa californica nuclear polyhedrosis virus (Ac M NPV) DNA. Two plaque-purified viruses, obtained from randomly picked plaques of a wild-type isolate of Ro M NPV, were recombinants of Ro M NPV and Ac M NPV. The recombinants were shown to have Ro M NPV and Ac M NPV restriction fragments as well as structural polypeptides from each parental virus. Both recombinant viruses had a major Ro M NPV capsid protein but were occluded in the Ac M NPV polyhedrin protein.

Groups of adenovirus type 2 mRNA's derived from a large primary transcript: probable nuclear origin and possible common 3' ends

Late in adenovirus type 2 infection, a number of mRNA's apparently arise by processing a large nuclear transcript that represents the right-hand 85% of the genome (summarized in Evans et al., Cell 12:733-739, 1977). Hybridization of labeled late mRNA to a series of DNA restriction fragments representing the right-hand 70% of the genome demonstrates at least 12 discrete mRNA's that appear to fall into five groups, each possibly containing a common 3' terminus. The processing necessary to generate these mRNA's apparently occurs in the nucleus. All the mRNA's appear to contain a sequence of approximately 100 nucleotides complementary to a fragment with coordinates 25.5-27.9. This fragment contains one of the regions found by Berget et al. (Proc. Natl. Sci. U.S.A. 74:3171-3175, 1977), Chow et al. (Cell 12:1-18, 1977), and Klessig (Cell 12:9-22, 1977) to the "spliced" onto the 5' end of late adenovirus type 2 mRNA's. Because the sequences to be spliced exist only once per large transcript, any of the mRNA-specific regions might only be preserved from a small fraction of the transcripts. Measurement of the transport efficiency of regions of the large nuclear transcript, if fact, shows that only 15 to 25% of any particular region is transported to the cytoplasm. The overall conclusion of these experiments is that the large late nuclear transcript can be processed in the nucleus to yield any one of many (approximately 12) mRNA's; the unused portions of the primary transcript then accumulate in the nucleus or are destroyed.

Assembly intermediates among adenovirus type 5 temperature-sensitive mutants

Temperature-sensitive mutants from three different complementation groups, ts5, ts19, and 6s58, have been shown to accumulate assembly intermediates at the restrictive temperature. The polypeptide composition of these intermediates is similar to that of the wild type, including the precursor polypeptides pVI, pVII, and pVIII. ts5 and ts19 also contained cleaved precursors, indicating assembly into defective virions. The increase of infectious virus after temperature shift-down of ts19 and ts58 was rapid when compared with that of ts24, which does not accumulate intermediates, suggesting that intermediates formed at nonpermissive temperature may be processed to mature virus. However, shift-down experiments reveal that only a fraction of the intermediates are utilized for virus assembly and that degradation of intermediates occurs at the restrictive temperature.

Species identification and genome mapping of cytoplasmic adenovirus type 2 RNAs synthesized late in infection

Adenovirus type 2 cytoplasmic RNAs synthesized late in productive infection were resolved by electrophoresis on formamide gels. Regions of the adenovirus 2 genome specifying RNAs of distinct size were determined by hybridization to specific DNA fragments generated by cleavage with endo R.EcoRI and endo R.SmaI. From these studies 13 distinct viral RNA species were identified. A 26S to 28S size class and a 21S to 23S size class were each found to consist of four distinct RNA species. Three RNA species were identified in a 16S to 18S size class, and a fourth size class, 11S to 13S, was resolved into two components. The SmaI-D region (0.38 to 0.51 on the unit genome) and the EcoRI-F, D region (0.70 to 0.83) of the genome were found to code for multiple transcripts. Three RNAs (28S, 22S, and 18S) are specified by SmaI-D, and four components, 28S, 22S, 18S, and 16S, are encoded by EcoRI-F,D. The RNA represented by each set of multiple transcripts exceeds the coding capacity of the respective region, and the species within each set of RNAs appear to contain common sequences. The relationship between the cytoplasmic RNA species synthesized at late times and early cytoplasmic RNAs was determined by hybridization-inhibition experiments. The multiple transcripts encoded by the EcoRI-D fragment were found to contain sequences that are present in early cytoplasmic RNA. These studies enabled preparation of a map which accounts for transcription of approximately 67% of the r strand of the adenovirus 2 genome.

Electron microscopy of late adenovirus type 2 mRNA hybridized to double-stranded viral DNA

R loops were generated with late adenovirus type 2 (Ad2) mRNA in double-stranded viral DNA, and visualized by electron microscopy. Unpaired DNA sequences in Ad2:Ad2+ND4 heteroduplex DNA served as a visual marker for the orientation of R loops with respect to the conventional DNA map. The most abundant classes of late Ad2 mRNA observed by this technique hybridized, in order of R-loop frequency, with midpoints near posit1ons 0.57, 0.88, 0.77, and 0.40 to 0.50 of the DNA map. The R loop at position 0.57, 0.88, 0.77, and 0.40 containing the hexon gene; the one at position 0.88 corresponded to a region containing the fiber gene. The relative frequencies of these two R loops paralleled those of the encoded gene products. The mRNA sizes, calculated from those of the respective R loops, were slightly larger than needed to code for these polypeptides. Using the R-loop technique, two locations at which adjacent mRNA's hybridized to different strands were accurately mapped at positions 0.61 and 0.91 of the DNA. The map positions of late Ad2 mRNA correlated well to published RNA and protein maps.

Visualization and mapping of late nuclear adenovirus RNA

Nuclei of KB cells harvested at late stages of productive infection with adenovirus type 2 (Ad2) harbor RNA molecules which measure up to 13 mum in length, as determined by electron microscopy of denatured RNA. While some of the molecules display features of secondary structure that are characteristic for precursor rRNA, our interest was in those showing almost no intramolecular folding. When hybridized to double stranded viral DNA under conditions which favor RNA:DNA duplex formation, nuclear AD2 RNA displaces the homologous DNA region and generates R loop structures whose size is proportional to the length of the hybridizing RNA. Slowly sedimenting RNA forms small R loops, whereas RNA of high sedimentation velocity generates loops that span a large proportion of the DNA length. Using SV40 sequences within Ad2+ND4 hybrid DNA as a position marker, we oriented many of the R loops on the conventional Ad2 map. Our analysis was restricted to the most abundant sequences of late Ad2 nuclear RNA participating in R loop formation. A small but significant proportion of large RNA generates loops between map positions 0.3 and 0.9. The much more frequent RNA of intermediate size (although larger than mRNA) hybridizes with midpoints near map positions 0.55 and 0.88--that is, near the gene locations for hexon and fiber. Our findings are compatible with the idea that the nuclear RNAs visualized in this study are intermediates in a processing pathway leading to mature forms of late Ad2 mRNA.

Restriction endonucleases

This review provides a comprehensive account of the current status of the biology and biochemistry of restriction endonucleases. Both Class I and Class II restriction endonucleases will be considered. However, emphasis will be placed on the Class II group, which recognizes and cleaves a specific duplex DNA sequence. Their occurrence, purification, and characterization is discussed in detail. The characterization includes physical mapping information and determination of recognition sequences. In addition to detailed discussions of the biochemical properties of the enzymes, considerable attention is paid to the uses of these enzymes as tools for research in molecular biology. These uses include physical mapping of genomes and their transcripts, genetic analysis (marker rescue, etc.), DNA sequence analysis, analysis of complex genomes, and genetic engineering. Specific examples of each use are outlined. Practical aspects of both the isolation and use of the restriction endonucleases form the major theme of this review.

Characterization of a temperature-sensitive, hexon transport mutant of type 5 adenovirus

Infection of KB cells at 39.5 degrees C with H5ts147, a temperature-sensitive (ts) mutant of type 5 adenovirus, resulted in the cytoplasmic accumulation of hexon antigen; all other virion proteins measured, however, were normally transported into the nucleus. Immunofluorescence techniques were used to study the intracellular location of viral proteins. Genetic studies revealed that H5ts147 was the single member of a nonoverlapping complementation group and occupied a unique locus on the adenovirus genetic map, distinct from mutants that failed to produce immunologically reactive hexons at 39.5 degrees C ("hexon-minus" mutants). Sedimentation studies of extracts of H5ts147-infected cells cultured and labeled at 39.5 degrees C revealed the production of 12S hexon capsomers (the native, trimeric structures), which were immunoprecipitable to the same extent as hexons synthesized in wild type (WT)-infected cells. In contrast, only 3.4S polypeptide chains were found in extracts of cells infected with the class of mutants unable to produce immunologically reactive hexon protein at 39.5 degrees C. Hexons synthesized in H5ts147-infected cells at 39.5 degrees C were capable of being assembled into virions, to the same extent as hexons synthesized in WT-infected cells, when the temperature was shifted down to the permissive temperature, 32 degrees C. Infectious virus production was initiated within 2 to 6 h after shift-down to 32 degrees C; de novo protein synthesis was required to allow this increase in viral titer. If ts147-infected cells were shifted up to 39.5 degrees C late in the viral multiplication cycle, viral production was arrested within 1 to 2 h. The kinetics of shutoff was similar to that of a WT-infected culture treated with cycloheximide at the time of shift-up. The P-VI nonvirion polypeptide, the precursor to virion protein VI, was unstable at 39.5 degrees C, whereas the hexon polypeptide was not degraded during the chase. It appears that there is a structural requirement for the transport of hexons into the nucleus more stringent than the acquisition of immunological reactivity and folding into the 12S form.