Studies on the bacteriophage MS 2

Summary The viral proteins synthesized in non-suppressor cells by amber mutants in the A protein cistron of the RNA bacteriophage MS2 were analyzed. Protein synthesis was studied in rifampicin-inhibited cultures and the labeled, viral proteins were separated on sodium dodecyl sulphate containing polyacrylamide gels. We found that 7 out of 19 mutants synthesized an A protein-fragment corresponding in length to 88% of the wild-type A protein. This fragment was not incorporated into the defective particles formed by the mutants. 12 mutants synthesized no detectable amount of fragment. It was shown that the absence of fragment is not due to selective proteolytic breakdown.     

Peptide epitope identification by affinity selection on bacteriophage MS2 virus-like particles

Filamentous phages are now the most widely used vehicles for phage display and provide efficient means for epitope identification. However, the peptides they display are not very immunogenic because they normally fail to present foreign epitopes at the very high densities required for efficient B-cell activation. Meanwhile, systems based on virus-like particles (VLPs) permit the engineered high-density display of specific epitopes but are incapable of peptide library display and affinity selection. We developed a new peptide display platform based on VLPs of the RNA bacteriophage MS2. It combines the high immunogenicity of MS2 VLPs with the affinity selection capabilities of other phage display systems. Here, we describe plasmid vectors that facilitate the construction of high-complexity random sequence peptide libraries on MS2 VLPs and that allow control of the stringency of affinity selection through the manipulation of display valency. We used the system to identify epitopes for several previously characterized monoclonal antibody targets and showed that the VLPs thus obtained elicit antibodies in mice whose activities mimic those of the selecting antibodies.     

Development of a microRNA delivery system based on bacteriophage MS2 virus-like particles

Recently, microRNA (miRNA)-mediated RNA interference has been developed as a useful tool in gene function analysis and gene therapy. A major obstacle in miRNA-mediated RNAi is cellular delivery, which requires an efficient and flexible delivery system. The self-assembly of the MS2 bacteriophage capsids has been used to develop virus-like particles (VLPs) for RNA and drug delivery. However, MS2 VLP-mediated miRNA delivery has not yet been reported. We therefore used an Escherichia coli expression system to produce the pre-miR 146a contained MS2 VLPs, and then conjugated these particles with HIV-1 Tat(47-57) peptide. The conjugated MS2 VLPs effectively transferred the packaged pre-miR146a RNA into various cells and tissues, with 0.92-14.76-fold higher expression of miR-146a in vitro and about two-fold higher expression in vivo, and subsequently suppressed its targeting gene. These findings suggest that MS2 VLPs can be used as a novel vehicle in miRNA delivery systems, and may have applications in gene therapy.     

Replication of bacteriophage MS2. X. Phage-specific ribonucleoprotein particles found in MS2-infected Escherichia coli

Phage-specific RNA-protein complexes formed during the MS2 infection process were examined. The fate of ³²P-labeled parental viral RNA was followed to determine what RNA-protein interactions developed early in infection. In order to identify phage-specific ribonucleoprotein complexes at later times in infection, their protein or RNA components were labeled selectively with radioisotopes after suppression of bacterial macromolecular syntheses with Miracil D (Burroughs Wellcome and Co.).     

Crystal packing of a bacteriophage MS2 coat protein mutant corresponds to octahedral particles

A covalent dimer of the bacteriophage MS2 coat protein was created by performing genetic fusion of two copies of the gene while removing the stop codon of the first gene. The dimer was crystallized in the cubic F432 space group. The organization of the asymmetric unit together with the F432 symmetry results in an arrangement of subunits that corresponds to T = 3 octahedral particles. The octahedral particles are probably artifacts created by the particular crystal packing. When it is not crystallized in the F cubic crystal form, the coat protein dimer appears to assemble into T = 3 icosahedral particles indistinguishable from the wild-type particles. To form an octahedral particle with closed surface, the dimer subunits interact at sharper angles than in the icosahedral arrangement. The fold of the covalent dimer is almost identical to the wild-type dimer with differences located in loops and in the covalent linker region. The main differences in the subunit packing between the octahedral and icosahedral arrangements are located close to the fourfold and fivefold symmetry axes where different sets of loops mediate the contacts. The volume of the wild-type virions is 7 times bigger than that of the octahedral particles.     

Structure and stability of icosahedral particles of a covalent coat protein dimer of bacteriophage MS2

Particles formed by the bacteriophage MS2 coat protein mutants with insertions in their surface loops induce a strong immune response against the inserted epitopes. The covalent dimers created by fusion of two copies of the coat protein gene are more tolerant to various insertions into the surface loops than the single subunits. We determined a 4.7‐Å resolution crystal structure of an icosahedral particle assembled from covalent dimers and compared its stability with wild‐type virions. The structure resembled the wild‐type virion except for the intersubunit linker regions. The covalent dimer orientation was random with respect to both icosahedral twofold and quasi‐twofold symmetry axes. A fraction of the particles was unstable in phosphate buffer because of assembly defects. Our results provide a structural background for design of modified covalent coat protein dimer subunits for use in immunization.     

Studies on the bacteriophage MS2: XXXIII. Comparison of the nucleotide sequences in related bacteriophage RNAs

We have recently determined the complete nucleotide sequence of the MS2 bacteriophage RNA molecule (Min Jou et al., 1972; Fiers et al., 1975,1976). Extensive segments of the sequence of the closely related phages R17 (23.9%) and f2 (11.5%) have been studied in other laboratories (Table 1). A comparison between the sequences of the phages MS2, R17 and f2 can now be given a functional significance by referring to the complete MS2 RNA sequence (Fig. 1).The estimation of the over-all degree of variation amounts to 3.9% (MS2-R17), 3.4% (MS2-f2) and 3.7% (R17-f2). All the differences observed can be accounted for by single base substitutions: transitions are highly predominant (86%). No change is found in the untranslated terminal regions and only two mutations occur in the intercistronic regions. From a total of 34 observed variable sites located in translated regions, 25 are neutral point mutations and only 9 lead to an (mostly rather conservative) amino acid change. The amount of variation in double-stranded regions (16 out of 36 cases) is much lower than the relative degree of secondary structure of the RNA (roughly two-thirds) would predict. Hence, there is clearly a selective pressure to preserve at least certain aspects of the three-dimensional conformation.     

Impact of iron particles in groundwater on the UV inactivation of bacteriophages MS2 and T4

AIMS: To investigate the impact of iron particles in groundwater on the inactivation of two model viruses, bacteriophages MS2 and T4, by 254-nm ultraviolet (UV) light. METHODS AND RESULTS: One-litre samples of groundwater with high iron content (from the Indianapolis Water Company, mean dissolved iron concentration 1.3 mg l(-1)) were stirred vigorously while exposed to air, which oxidized and precipitated the dissolved iron. In parallel samples, ethylenediaminetetra-acetic acid (EDTA) was added to chelate the iron and prevent formation of iron precipitate. The average turbidity in the samples without EDTA (called the 'raw' samples) after 210 min of stirring was 2.7 +/- 0.1 NTU while the average turbidity of the samples containing EDTA (called the 'preserved' samples) was 1.0 +/- 0.1 NTU. 'Raw' and 'preserved' samples containing bacteriophage MS2 were exposed to 254-nm UV light at doses of 20, 40, or 60 mJ (cm(2))(-1), while samples containing bacteriophage T4 were exposed to 2 or 5 mJ (cm(2))(-1), using a low pressure UV collimated beam. The UV inactivation of both phages in the 'raw' groundwater was lower than in the EDTA-'preserved' groundwater to a statistically significant degree (alpha = 0.05), due to the association of phage with the UV-absorbing iron precipitate particles. A phage elution technique confirmed that a large fraction of the phage that survived the UV exposures were particle-associated. CONCLUSIONS: Phages that are associated with iron oxide particles in groundwater are shielded from UV light to a measurable and statistically significant degree at a turbidity level of 2.7 NTU when the phage particle association is induced under experimental conditions. SIGNIFICANCE AND IMPACT OF THE STUDY: While the particle association of the phage in this study was induced experimentally, the findings provide further evidence that certain particles in natural waters and wastewaters (e.g. iron oxide particles) may have the potential to shield viruses from UV light.     

Studies on the bacteriophage MS2: XLI. Nature of the azure mutation

Azure (or reverse amber) mutants grow normally on wild-type Escherichia coli but not on host strains harbouring a strong UAG suppressor mutation. Three different bacteriophage MS2 azure mutants obtained by treatment with nitrous acid have been characterized at the nucleotide sequence level. The 3′-end fragment of the ³²P-labelled mutant genomes was isolated by DNA:RNA hybridization and treatment with nuclease S₁, and was analyzed by mini-fingerprinting of the RNA. It is known that the wild-type MS2 polymerase gene ends with a UAG codon, followed seven triplets further by an in-phase UAA triplet. All three azure mutants contained an A → G transition in this UAA second stop codon of the polymerase gene, resulting in a second suppressible UAG (amber) codon. Analysis of revertants demonstrated that the azure mutation can be counteracted either by a true site reversion at the second stop or by the creation of a new stop signal for the polymerase gene, either UAA (ochre) or UGA (opal), before or at the first stop, or beyond the second stop. On the basis of these results, a mechanism for the azure mutation is proposed. Silent mutations (one in the coding region, three in the untranslated 3′-terminal sequence) have also been observed in these phage stocks.     

Null and electrophoretic mobility mutants in the structural gene for L-lactate dehydrogenase of Saccharomyces cerevisiae

A mutant lacking L-lactate dehydrogenase (EC 1.1.2.3) of Saccharomyces cerevisiae was isolated by its inability to grow on minimal medium with L-lactate as a carbon source. A simple activity gel assay for visualization of this enzyme and the two D-lactate dehydrogenases in this organism (EC 1.1.2.4 and 1.1.1.28) was developed. This enabled us to screen spontaneous and ethylmethanesulfonate-induced back mutants for electrophoretic mobility. Two mutants with a mobility faster than that of the wild type were isolated, and proved to be allelic to the L-lactate dehydrogenase negative mutant.     

Studies on the bacteriophage MS2. XXII. Conformation of MS2 RNA in acid medium

MS2 RNA, which sediments at 27S in a neutral buffer, can be converted to a compact 57S conformation at pH 3.8. Requirements for this conversion, besides protonation, are small concentrations of Mg⁺⁺ ions and a low ionic strength. On the other hand, after heating in the presence of EDTA and at low ionic strength, the RNA can be unfolded to an 11.7S form at pH 6.8 and to 10.5S at pH 3.8. The compact 57S form has lost at least 50% of its secondary structure, as determined by its hypochromicity. It corresponds to a monomer species, as will be shown in a following paper (XXIV). Comparative studies with the homopolymers poly A and poly C and with the heteropolymers poly A,U, poly A,C, and poly A,G indicate that the interactions involved in the acid RNA conformation are not simply explainable by the known interactions of the A–A⁺, C–C⁺, and/or A–C⁺ type.     

The effects of calcium2+ and magnesium2+ on the electrophoretic mobility of chromaffin granules measured by electrophoretic light scattering

Electrophoretic light scattering was used to determine the electrophoretic mobility distributions of isolated bovine adrenal chromaffin granules as a function of divalent metal ion concentrations. Changes in the electrophoretic mobility reflected changes in the surface charge density of the granules. Ca2+ and Mg2+ (0.10--2.0 mM) were equally effective in reducing the electrophoretic mobilities. These findings are consistent with recent studies of the binding of Ca2+ and Mg2+ to the surface of chromaffin granules and are further evidence that the specific role of Ca2+ in exocytosis is due to effects other than the ability of Ca2+ to decrease the electrostatic repulsion between negatively charged membranes.     

Studies on the bacteriophage MS2. XXIV. Hydrodynamic properties of the native and acid MS2 RNA structures

The molecular weight of native 26.6S MS2 RNA, of acidic 53.1S MS2 RNA and of formaldehyde-treated 36.1S MS2 RNA was determined by light-scattering studies. The three forms examined correspond to monomers. Also νv values were determined, and in conjunction with our previous estimates for S_20,W and [η], led again to the conclusion that formaldehyde-cross-linked 37S MS2 RNA is a monomer. On the basis of the experimentally observed R_G, [η], S_20,W, and νv values, and taking a prolate ellipsoid as a model, the hydrodynamic volume, the solvation water and the axial ratio could be deduced for the three conformations. In the “native” 26S form the RNA occupies only 8.2% of the hydrodynamic volume. The formation of the 36S and the 53S structures correspond largely to a loss of solvation water.     

Surface charge of eosinophils. Binding of cationic particles and measurement of cellular electrophoretic mobility

Summary The surface charge of eosinophils, isolated from the peritoneal exudate of rats by the use of a Metrizamide gradient, was analysed by ultrastructural cytochemistry and cellular electrophoretic mobility. Binding of colloidal iron hydroxide and of cationized ferritin particles at pH 1.8 and 7.2 respectively, was observed on the surface of the eosinophils. An electrophoretic mobility of –1.08 and –1.39 m·s^–1·V^–1·cm was determined for living and glutaraldehyde-fixed eosinophils, respectively. Treatment of the cells with neuraminidase reduced the electrophoretic mobility to –0.64 m·s^–1·V^–1·cm (glutaraldehyde-fixed), reduced significantly and abolished completely the binding of both colloidal iron hydroxide and cationized ferritin particles to the surface of the cells. These results indicate that sialic acid exists on the surface of eosinophils, where it accounts for part of the negative surface charge.