Localisation of a high affinity binding site for coat protein on the 3′-terminal part of RNA 4 of alfalfa mosaic virus

Viral genomic single-stranded RNA directs the pathway toward a T=3 capsid

The molecular mechanisms controlling genome packaging by single-stranded RNA viruses are still largely unknown. It is necessary in most cases for the protein to adopt different conformations at different positions on the capsid lattice in order to form a viral capsid from multiple copies of a single protein. We showed previously that such quasi-equivalent conformers of RNA bacteriophage MS2 coat protein dimers (CP(2)) can be switched by sequence-specific interaction with a short RNA stem-loop (TR) that occurs only once in the wild-type phage genome. In principle, multiple switching events are required to generate the phage T=3 capsid. We have therefore investigated the sequence dependency of this event using two RNA aptamer sequences selected to bind the phage coat protein and an analogous packaging signal from phage Qbeta known to be discriminated against by MS2 coat protein both in vivo and in vitro. All three non-cognate stem-loops support T=3 shell formation, but none shows the kinetic-trapping effect seen when TR is mixed with equimolar CP(2). We show that this reflects the fact that they are poor ligands compared with TR, failing to saturate the coat protein under the assay conditions, ensuring that sufficient amounts of both types of dimer required for efficient assembly are present in these reactions. Increasing the non-cognate RNA concentration restores the kinetic trap, confirming this interpretation. We have also assessed the effects of extending the TR stem-loop at the 5' or 3' end with short genomic sequences. These longer RNAs all show evidence of the kinetic trap, reflecting the fact that they all contain the TR sequence and are more efficient at promoting capsid formation than TR. Mass spectrometry has shown that at least two pathways toward the T=3 shell occur in TR-induced assembly reactions: one via formation of a 3-fold axis and another that creates an extended 5-fold complex. The longer genomic RNAs suppress the 5-fold pathway, presumably as a consequence of steric clashes between multiply bound RNAs. Reversing the orientation of the extension sequences with respect to the TR stem-loop produces RNAs that are poor assembly initiators. The data support the idea that RNA-induced protein conformer switching occurs throughout assembly of the T=3 shell and show that both positional and sequence-specific effects outside the TR stem-loop can have significant impacts on the precise assembly pathway followed.

Roles of operator and non-operator RNA sequences in bacteriophage R17 capsid assembly

In order to understand the role of sequences other than the translational operator on bacteriophage R17 assembly, in vitro capsid assembly was studied with R17 coat protein and a variety of RNAs. For a series of RNA oligomers of the same chain length, sequences that bind coat protein dimer with a lower affinity require higher concentrations of RNA and protein for assembly. Among a series of non-specific RNA molecules of differing lengths, lower protein and RNA concentrations are required for assembly of capsids containing longer RNAs. For RNA molecules of any length, the presence of a single high-affinity translational operator sequence lowered the concentration requirements for capsid assembly. However, the advantage for encapsidation provided by the operator sequence is small for large RNA molecules. The experiments indicate that in the overall assembly process the interaction of coat protein with non-specific sequences is at least as important as its interaction with the specific translational operator sequence. In light of the data, a mechanism of achieving selective packaging of the R17 genomic RNA in vivo is discussed.

Protein binding sites in nucleation complexes of alfalfa mosaic virus RNA 4

The subgenomic coat protein messenger RNA 4 of alfalfa mosaic virus forms complexes with one and three coat protein dimers, which are designated complexes I and III, respectively. These complexes were separated, subjected to digestion with ribonuclease T1, and filtered onto Millipore filters. Phenol extracts of the filters contained specific fragments of RNA 4, which were sequenced after electrophoretic separation on nondenaturing and denaturing polyacrylamide gels. Complex I yielded only a 68-nucleotide fragment including the 3' terminus [fragment 814-881 according to the numbering of Brederode, F. Th., Koper-Zwarthoff, E. C., & Bol, J. F. (1980) Nucleic Acids Res. 8, 2213-2223]. Complex III yielded in addition to the former fragment also other, mostly extracistronic, fragments from the 3'-terminal region, as well as fragments from an intracistronic region, comprising positions 425-474, in the middle of RNA 4. The 3'-terminal region was subdivided by small gaps into three coat protein binding sites: 799-881, 759-787, and 667-753, designated sites 1, 2, and 3, respectively, and possibly representing the sites occupied by the three coat protein dimers. A similarity may exist between the secondary structure of sites 1 and 3, which both may have three hairpins, two of which flanked at their 3' side by an AUGC sequence. Furthermore, a complementarity was noted between the loop of a large hairpin which can be drawn in the intracistronic site and the upper part of one of the three hairpins in the 3'-terminal site 1. These binding features have been combined in a model structure for the complex of RNA 4 with three coat protein dimers.

Alterations of the conformation of the RNAs of alfalfa mosaic virus upon binding of a few coat protein molecules

Structural changes in the single-stranded genome RNAs (RNAs 1, 2 and 3) and the subgenomic coat protein messenger (RNA 4) of alfalfa mosaic virus upon addition of a few coat protein molecules of the virus were investigated by measuring the fluorescent intensity of bound ethidium bromide and by circular dichroism. No effect could be observed in the case of the genome RNAs. However, in RNA 4, which is of much less complexity than the genome RNAs, a reduction of the ethidium bromide binding by 30% was found, whereas the positive molar ellipticity at 265 nm was reduced by 9% upon binding of the coat protein. Both changes point to a reduction of the ordered structure of the RNA. Since the protein is known to bind first at the 3'-terminus of RNA 4 and probably also of the genome RNAs, the conformational changes observed could be those thought to be necessary for replicase recognition in this positive-stranded RNa virus which needs the coat protein for starting an infection cycle.