Dissecting the Fine Details of Assembly of aT = 3 Phage Capsid

Packaging of Genomic RNA in Positive-Sense Single-Stranded RNA Viruses: A Complex Story

The packaging of genomic RNA in positive-sense single-stranded RNA viruses is a key part of the viral infectious cycle, yet this step is not fully understood. Unlike double-stranded DNA and RNA viruses, this process is coupled with nucleocapsid assembly. The specificity of RNA packaging depends on multiple factors: (i) one or more packaging signals, (ii) RNA replication, (iii) translation, (iv) viral factories, and (v) the physical properties of the RNA. The relative contribution of each of these factors to packaging specificity is different for every virus. In vitro and in vivo data show that there are different packaging mechanisms that control selective packaging of the genomic RNA during nucleocapsid assembly. The goals of this article are to explain some of the key experiments that support the contribution of these factors to packaging selectivity and to draw a general scenario that could help us move towards a better understanding of this step of the viral infectious cycle.

Symmetry-adapted digital modeling III. Coarse-grained icosahedral viruses

Considered is the coarse-grained modeling of icosahedral viruses in terms of a three-dimensional lattice (the digital modeling lattice) selected among the projected points in space of a six-dimensional icosahedral lattice. Backbone atomic positions (Cα's for the residues of the capsid and phosphorus atoms P for the genome nucleotides) are then indexed by their nearest lattice point. This leads to a fine-grained lattice point characterization of the full viral chains in the backbone approximation (denoted as digital modeling). Coarse-grained models then follow by a proper selection of the indexed backbone positions, where for each chain one can choose the desired coarseness. This approach is applied to three viruses, the Satellite tobacco mosaic virus, the bacteriophage MS2 and the Pariacoto virus, on the basis of structural data from the Brookhaven Protein Data Bank. In each case the various stages of the procedure are illustrated for a given coarse-grained model and the corresponding indexed positions are listed. Alternative coarse-grained models have been derived and compared. Comments on related results and approaches, found among the very large set of publications in this field, conclude this article.

RNA-induced conformational changes in a viral coat protein studied by hydrogen/deuterium exchange mass spectrometry

A detailed knowledge of the capsid assembly pathways of viruses from their coat protein building blocks is required to devise novel therapeutic strategies to inhibit such assembly. In the quest for understanding how assembly of single-stranded RNA viruses is achieved at the molecular level, HDX-MS has been used to locate regions of a coat protein dimer that exhibit conformational/dynamical changes, and hence changes in their HDX kinetics, upon binding to a genomic RNA stem-loop known to trigger assembly initiation. The HDX-MS data highlight specific areas within the coat protein dimer that alter their exchange kinetics in the presence of the RNA. These include the known RNA-binding sites, β-strands E and G, which have a lower susceptibility to HDX when ligand-bound, as may have been expected. In contrast, several exposed regions are unaffected by ligand binding. Significantly in this example, the loop between β-strands F and G exhibits reduced HDX propensity when the RNA is bound, consistent with previous inferences from NMR and normal mode analysis that suggested a local conformational change at this loop induced by dynamic allostery. These results demonstrate the potential utility of HDX to probe conformational and dynamical changes within non-covalently bound protein-ligand complexes which are of widespread importance in many biomolecular systems.

Determining the topology of virus assembly intermediates using ion mobility spectrometry-mass spectrometry

We have combined ion mobility spectrometry-mass spectrometry with tandem mass spectrometry to characterise large, non-covalently bound macromolecular complexes in terms of mass, shape (cross-sectional area) and stability (dissociation) in a single experiment. The results indicate that the quaternary architecture of a complex influences its residual shape following removal of a single subunit by collision-induced dissociation tandem mass spectrometry. Complexes whose subunits are bound to several neighbouring subunits to create a ring-like three-dimensional (3D) architecture undergo significant collapse upon dissociation. In contrast, subunits which have only a single neighbouring subunit within a complex retain much of their original shape upon complex dissociation. Specifically, we have determined the architecture of two transient, on-pathway intermediates observed during in vitro viral capsid assembly. Knowledge of the mass, stoichiometry and cross-sectional area of each viral assembly intermediate allowed us to model a range of potential structures based on the known X-ray structure of the coat protein building blocks. Comparing the cross-sectional areas of these potential architectures before and after dissociation provided tangible evidence for the assignment of the topologies of the complexes, which have been found to encompass both the 3-fold and the 5-fold symmetry axes of the final icosahedral viral shell. Such insights provide unique information about virus assembly pathways that could allow the design of anti-viral therapeutics directed at the assembly step. This methodology can be readily applied to the structural characterisation of many other non-covalently bound macromolecular complexes and their assembly pathways.

Assembly of mixed rod-like and spherical particles from group I and II RNA bacteriophage coat proteins

The capsids of single-stranded RNA bacteriophages show remarkable structural similarity. In an attempt to test whether the coat protein (CP) from one bacteriophage could substitute for the CP of another and form mixed particles, we reassembled capsids in vitro from a mixture of different RNA phage CP dimers together with E. coli ribosomal RNA. Surprisingly, mixing CPs from phages belonging to groups I and II led to appearance of rod-like particles along with icosahedral spherical capsids, both containing a mixture of the two CPs. Rods and mixed spherical capsids containing host RNA were also obtained in vivo in bacteria expressing simultaneously fr and GA CPs. In a co-infection of the two phages, however, only authentic fr and GA virions were formed. Coat protein mutants in the FG loop were unable to assemble into rods, suggesting that these loops are involved in the formation of the aberrant particles.

Insights into virus capsid assembly from non-covalent mass spectrometry

The assembly of viral proteins into a range of macromolecular complexes of strictly defined architecture is one of Nature's wonders. Unraveling the details of these complex structures and the associated self-assembly pathways that lead to their efficient and precise construction will play an important role in the development of anti-viral therapeutics. It will also be important in bio-nanotechnology where there is a plethora of applications for such well-defined macromolecular complexes, including cell-specific drug delivery and as substrates for the formation of novel materials with unique electrical and magnetic properties. Mass spectrometry has the ability not only to measure masses accurately but also to provide vital details regarding the composition and stoichiometry of intact, non-covalently bound macromolecular complexes under near-physiological conditions. It is thus ideal for exploring the assembly and function of viruses. Over the past decade or so, significant advances have been made in this field, and these advances are summarized in this review, which covers the literature up to the end of 2007.

The three-dimensional structure of genomic RNA in bacteriophage MS2: implications for assembly

Using cryo-electron microscopy, single particle image processing and three-dimensional reconstruction with icosahedral averaging, we have determined the three-dimensional solution structure of bacteriophage MS2 capsids reassembled from recombinant protein in the presence of short oligonucleotides. We have also significantly extended the resolution of the previously reported structure of the wild-type MS2 virion. The structures of recombinant MS2 capsids reveal clear density for bound RNA beneath the coat protein binding sites on the inner surface of the T=3 MS2 capsid, and show that a short extension of the minimal assembly initiation sequence that promotes an increase in the efficiency of assembly, interacts with the protein capsid forming a network of bound RNA. The structure of the wild-type MS2 virion at approximately 9 A resolution reveals icosahedrally ordered density encompassing approximately 90% of the single-stranded RNA genome. The genome in the wild-type virion is arranged as two concentric shells of density, connected along the 5-fold symmetry axes of the particle. This novel RNA fold provides new constraints for models of viral assembly.

A simple, RNA-mediated allosteric switch controls the pathway to formation of a T=3 viral capsid

Using mass spectrometry we have detected both assembly intermediates and the final product, the T=3 viral capsid, during reassembly of the RNA bacteriophage MS2. Assembly is only efficient when both types of quasiequivalent coat protein dimer seen in the final capsid are present in solution. NMR experiments confirm that interconversion of these conformers is allosterically regulated by sequence-specific binding of a short RNA stem-loop. Isotope pulse-chase experiments confirm that all intermediates observed are competent for further coat protein addition, i.e., they are all on the pathway to capsid formation, and that the unit of capsid growth is a coat protein dimer. The major intermediate species are dominated by stoichiometries derived from formation of the particle threefold axis, implying that there is a defined pathway toward the T=3 shell. These results provide the first experimental evidence for a detailed mechanistic explanation of the regulation of quasiequivalent capsid assembly. They suggest a direct role for the encapsidated RNA in assembly in vivo, which is consistent with the structure of the genomic RNA within wild-type phage.

Cryo electron microscopy reconstructions of the Leviviridae unveil the densest icosahedral RNA packing possible

We solved the structures of the single-stranded RNA bacteriophages Qbeta, PP7 and AP205 by cryo-electron microscopy. On the outside, the symmetrized electron density maps resemble the previously described cryo-electron microscopy structure of MS2. RNA density is present inside the capsids, suggesting that the genomic RNA of Qbeta, PP7 and AP205, analogous to MS2, contains many coat protein-binding sites in addition to the hairpin on which assembly and packaging are initiated. All four bacteriophages harbour the same overall arrangement of the RNA, which is a unique combination of both triangles and pentagons. This combination has not been found in other icosahedral viruses, in which the RNA structures are either triangular or pentagonal. Strikingly, the unique RNA packing of the Leviviridae appears to deploy the most efficient method of RNA storage by obeying icosahedral symmetry.