Isolation of an infectious RNA-A-protein complex from the bacteriophage M12

Structures of Qβ virions, virus-like particles, and the Qβ-MurA complex reveal internal coat proteins and the mechanism of host lysis

In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the canonical Allolevivirus Qβ the maturation protein, A₂, has an additional role as the lysis protein, by its ability to bind and inhibit MurA, which is involved in peptidoglycan biosynthesis. Here, we determined structures of Qβ virions, virus-like particles, and the Qβ-MurA complex using single-particle cryoelectron microscopy, at 4.7-Å, 3.3-Å, and 6.1-Å resolutions, respectively. We identified the outer surface of the β-region in A₂ as the MurA-binding interface. Moreover, the pattern of MurA mutations that block Qβ lysis and the conformational changes of MurA that facilitate A₂ binding were found to be due to the intimate fit between A₂ and the region encompassing the closed catalytic cleft of substrate-liganded MurA. Additionally, by comparing the Qβ virion with Qβ virus-like particles that lack a maturation protein, we observed a structural rearrangement in the capsid coat proteins that is required to package the viral gRNA in its dominant conformation. Unexpectedly, we found a coat protein dimer sequestered in the interior of the virion. This coat protein dimer binds to the gRNA and interacts with the buried α-region of A₂, suggesting that it is sequestered during the early stage of capsid formation to promote the gRNA condensation required for genome packaging. These internalized coat proteins are the most asymmetrically arranged major capsid proteins yet observed in virus structures.

The three-dimensional structure of bacteriophage PP7 from Pseudomonas aeruginosa at 3.7-A resolution

The three-dimensional structure of phage PP7 from Pseudomonas aeruginosa has been determined to 3.7-A resolution. A comparison with distantly related small RNA phages showed that the biggest differences were found in the FG loops, forming the contacts around the fivefold and threefold axes. In contrast to the situation in other phages, the FG loops of phage PP7 are very similar in all three subunits. This supports the hypothesis that no switches are needed for the assembly control in these viruses. Some of the most conserved residues lie within the region involved in RNA binding in the related phages MS2 and seem to have the same function.

Localization of A protein in the RNA-A protein complex of RNA phage MS2

The site of interaction of phage MS2 A protein on MS2 RNA was determined by analysing the base sequence of the RNA fragment which was released from the RNAase-resistant complex prepared by RNAase digestion of RNA-A protein complex. The result showed that there were two types of RNA fragment: one had a sequence which corresponded to the sequence of the 5'-side maturation region of MS2 RNA and the other corresponded to the sequence of the 3'-side untranslated region. These results were confirmed by a competition experiment in in vitro reconstitution system using f2 defective RNA, lacking about 30% of the 5'-side, and MS2 5FUra (5-fluorouracil) RNA, lacking about 35% of the 3'-side, as competitors. These results seem to indicate that the A protein is bound to at least two sites on MS2 RNA.

Leakage induced in Escherichia coli cells by A protein-RNA complexes from bacteriophage f2

Complexes of f2 phage RNA and its A protein, or maturation protein, transfect Escherichia coli cells much better than does protein-free RNA. We used these complexes to introduce the bacteriophage f2 lysis gene into cells. The A protein-RNA complex was found to kill cells, probably by causing them to leak large macromolecules. Previously induced beta-galactosidase leaked from cells treated either with the A protein-RNA complex or with lethal but noninfectious complexes that had been treated with formaldehyde. This observation was consistent with an earlier finding that formaldehyde-treated f2 RNA stimulates the in vitro synthesis of a lysis protein. The complexes did not stimulate the rate of leakage of beta-galactosidase from a streptomycin-resistant mutant known to be lysis defective. On the other hand, the rate of leakage was increased in a double mutant resistant to both streptomycin and rifampin and which is lysed normally by f2 bacteriophage.