Bernard Jacrot

The sequence of the genome of adenovirus type 5 and its comparison with the genome of adenovirus type 2

We report the sequence of 7558 nucleotides of the adenovirus type 5 genome. With this sequence and previously published data, the complete sequence of this genome is now available and can be compared with the already known sequence of the adenovirus type 2 genome. These two serotypes belong to the same subgroup and sequence comparison shows 94.7% homology between the two genomes. The differences are not at all randomly distributed. Transitions between C and T and between A and G account in total for 58.3% of the differences and even for 68.6% for the genome devoid of the fiber and the hexon genes (instead of 33% expected for an equal probability of changes). In the fiber gene the transitions account for 47% of the differences. The detailed analysis of the nucleotide substitution between the two genomes suggests that the Ad2 genome could derive from that of Ad5 one, with the exception of the fiber gene which is likely to be present in Ad2 genome as a result of genetic recombination. The homology between the amino acids sequences of the structural proteins varies from 100% (proteins pVII and IX) to only 69.2% for the fiber.

Crystallization, enzymatic cleavage, and the polarity of the adenovirus type 2 fiber

Crystals of the fiber protein of adenovirus type 2 have been grown. Analysis of these crystals (type I crystals) showed that they were composed of fiber polypeptide with a lower apparent molecular weight (60 kDa) than that of the soluble or virion-incorporated fiber (62 kDa). N-terminal sequencing revealed that the fiber polypeptide chain of 60 kDa was cleaved at tyrosine17 from the N-end. The C-terminus remained intact. Assays with protease inhibitors suggested that the spontaneous cleavage of the fiber occurring upon its crystallization was due to a cellular, calcium-dependent, chymotrypsin-like protease co-purifying with the fiber and activated during hydroxyapatite chromatography. Crystallization of fiber purified in the presence of chymostatin provided crystals of a different structure under the electron microscope (crystals of type II), composed of 62-kDa fiber polypeptide units. The 62-kDa fiber from the type II crystals, as well as the 62-kDa fiber isolated from infected cell extracts, were able to associate with the penton base in vitro to form a penton capsomer. The 60-kDa fiber has lost this capacity. The accessibility of the N- and C-termini of the fiber inside the penton structure was probed by anti-peptide sera after limited proteolysis. The results are consistent with a polarity of the fiber in which its N-terminus is oriented toward the penton base, the C-terminal domain corresponding to the distal knob.

The sequence of adenovirus fiber: Similarities and differences between serotypes 2 and 5

The amino acid sequence of the fiber from adenovirus type 5 has been deduced from the nucleotide sequence of the fiber gene. This sequence is compared with that of adenovirus type 2, a closely related serotype. We find 69% homology for the fiber protein whereas the known nonstructural proteins of these two serotypes have 99% sequence homology. A detailed sequence analysis was performed in the context of the model proposed by Green et al., [(1983), EMBO J., 8, 1357-1365] for the folding of the polypeptide chain of the adenovirus type 2 fiber. The N-terminal region, which in the virion is associated with the capsid, is identical for these two serotypes. In the shaft of the fiber the features, such as periodicity of the prolines and of the hydrophobic residues in the amino acid sequence, on which the model for the adenovirus type 2 is based are very well preserved in adenovirus type 5. On the other hand, there are large differences all along the sequence of the shaft of the fiber showing that there is a very limited homology between the amino acids in the two serotypes when they do not have a key role in establishing the structure. In the knob the homology between serotypes is 64%. These results are consistent with the differences between serotypes being confined to the exposed proteins.

Determination of the nucleotide sequence for the penton-base gene of human adenovirus type 5

The major structural proteins of adenovirus (Ad), which form the external capsid, are hexon, penton base and fiber. The primary structure of the Ad5 penton base has been deduced from the nucleotide sequence of the corresponding gene. It has 98.6% homology with the sequence of the analogous protein from Ad2. This result is in contrast with the significantly lower homology found for the two other major structural proteins, the hexon and the fiber.

A T = 1 capsid formed by protein of brome mosaic virus in the presence of trypsin

In the presence of trypsin, the coat protein of brome mosaic virus (BMV) has been observed to polymerize in a D2O buffer at pD 7.6 to form a small empty capsid with triangulation number T = 1. Normally, this same protein polymerizes at acidic pH to form empty capsids with T = 3. The trypsin is shown to remove 63 amino acids on the N terminus side leaving a polypeptide chain of Mr 13,500. The kinetics of formation of this small particle have been followed by neutron scattering. Further, the particle has been characterized by various physical methods: analytical centrifugation, quasielastic light scattering, and neutron scattering. It is found to have a radius of about 85-90 A, and a molecular weight of 760,000, in fair agreement with the value expected for a particle made of 60 subunits of 13,500.

Self-assembly of brome mosaic virus protein into capsids: Initial and final states of aggregation

The pH and ionic strength dependence of the states of aggregation of brome mosaic virus protein has been investigated by small angle neutron scattering, quasielastic light-scattering, analytical centrifugation and electron microscopy. At pH above neutrality, protein oligomers are found in dynamical equilibrium, comprising monomers, dimers and aggregates of higher molecular weight. By lowering the pH, capsids assemble spontaneously with dimensions in solution which depend on ionic strength. If formed by dialysis, they contain 180 monomers, but are 30 A larger in diameter than the native virus. If formed by pH-jump, they contain less monomers: the deficiency decreases with decreasing the final pH and the initial protein concentration. Upon dehydration for electron microscopy, capsids contract by 10%.

The penton base of human adenovirus type 3 has the RGD motif.

The gene encoding the penton base of human adenovirus (Ad) type 3 has been sequenced. The resulting amino-acid sequence has an Arg-Gly-Asp (RGD) motif located near its middle in a hydrophilic region. The same motif is found in serotypes 2, 5 and 12. This sequence was found [Wickham et al., Cell 73 (1993) 309-319] to be involved in the internalisation of Ad2 through an interaction with some specific integrins.

Molecular weight of adenovirus serotype 2 capsomers. A new characterization.

Abstract We have determined the molecular weight of some of the adenovirus serotype 2 structural proteins: penton, penton base and fibre. Physical techniques, namely neutron scattering and hydrodynamical measurements, indicate that the penton base is a trimer. This is confirmed by analysis of the virion composition based on quantitative gel scanning. This finding implies either that other proteins (e.g. protein IIIa) are essential in the architecture of the fivefold vertex of the virion, or that the usual assumption that icosahedral symmetry involves identical interactions related to the symmetry of the virion does not hold.

Crystal packing and stoichiometry of the fibre protein of adenovirus type 2

Crystals of the fibre protein of adenovirus type 2 have been grown and studied by electron microscopy and X-ray powder diffraction. The molecular packing and density of the crystals suggest that the fibre is dimeric.

Effect of dinucleotides on wheat germ translation system

The effect of ribodinucleoside monophosphates on total protein synthesis was studied in a wheat germ cellfree system, using brome mosaic virus (BMV) RNA as a messenger. Dinucleotides inhibit total protein synthesis to different extents. Of those tested the most inhibitory is CpA. The inhibitory effect of dinucleotides is due to their adverse effect on initiation and not on elongation of polypeptide synthesis. It seems that the dinucleotides complementary to the initiation codon are able to compete with the initiator tRNA during initiation of protein synthesis. The comparison of the effect exerted by different dinucleotides suggests that under conditions of the in vitro protein synthesis RNA 4 is an mRNA molecule with the initiation codon and its immediate neighbourhood being exposed.