Single-stranded RNA phages ToC (original) (raw)
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The True Story and Advantages of RNA Phage Capsids as Nanotools
RNA phages are often used as prototypes for modern recombinant virus-like particle (VLP) technologies. Icosahedral RNA phage VLPs can be formed from coat proteins (CPs) and are efficiently produced in bacteria and yeast. Both genetic fusion and chemical coupling have been successfully used for the production of numerous chimeras based on RNA phage VLPs. In this review, we describe advances in RNA phage VLP technology along with the history of the Leviviridae family, including its taxonomical organization, genomic structure, and important role in the development of molecular biology. Comparative 3D structures of different RNA phage VLPs are used to explain the level of VLP tolerance to foreign elements displayed on VLP surfaces. We also summarize data that demonstrate the ability of CPs to tolerate different organic (peptides, oligonucleotides, and carbohydrates) and inorganic (metal ions) compounds either chemically coupled or noncovalently added to the outer and/or inner surfaces of VLPs. Finally, we present lists of nanotechnological RNA phage VLP applications, such as experimental vaccines constructed by genetic fusion and chemical coupling methodologies, nanocontainers for targeted drug delivery, and bioimaging tools.
Rapid de novo evolution of lysis genes in single-stranded RNA phages
Nature Communications, 2020
Leviviruses are bacteriophages with small single-stranded RNA genomes consisting of 3-4 genes, one of which (sgl) encodes a protein that induces the host to undergo autolysis and liberate progeny virions. Recent meta-transcriptomic studies have uncovered thousands of leviviral genomes, but most of these lack an annotated sgl, mainly due to the small size, lack of sequence similarity, and embedded nature of these genes. Here, we identify sgl genes in 244 leviviral genomes and functionally characterize them in Escherichia coli. We show that leviviruses readily evolve sgl genes and sometimes have more than one per genome. Moreover, these genes share little to no similarity with each other or to previously known sgl genes, thus representing a rich source for potential protein antibiotics.
RNA Phage VLP-Based Vaccine Platforms
Pharmaceuticals
Virus-like particles from a variety of RNA bacteriophages have turned out to be useful platforms for delivery of vaccine antigens in a highly immunogenic format. Here we update the current state of development of RNA phage VLPs as platforms for presentation of diverse antigens by genetic, enzymatic, and chemical display methods.
Immunogenic Display of Diverse Peptides on Virus-like Particles of RNA Phage MS2
Journal of Molecular Biology, 2008
The high immunogenicity of peptides displayed in dense repetitive arrays on virus-like particles makes recombinant VLPs promising vaccine carriers. Here we describe a platform for vaccine development based on the VLPs of RNA bacteriophage MS2. It serves for the engineered display of specific peptide sequences, but will also allow the construction of random peptide libraries from which specific binding activities can be recovered by affinity selection. Peptides representing the V3 loop of HIV gp120 and the ECL2 loop of the HIV coreceptor, CCR5, were inserted into a surface loop of MS2 coat protein. Both insertions disrupted coat VLP assembly, apparently by interfering with protein folding, but these defects were efficiently suppressed by genetically fusing coat protein's two identical polypeptides into a single-chain dimer. The resulting VLPs displayed the V3 and ECL2 peptides on their surfaces where they showed the potent immunogenicity that is the hallmark of VLPdisplayed antigens. Experiments with random-sequence peptide libraries show the single-chain dimer to be highly tolerant of 6-, 8-and 10-amino acid insertions. Not only do MS2 VLPs support the display of a wide diversity of peptides in a highly immunogenic format, but they also encapsidate the mRNAs that direct their synthesis, thus establishing the genotype/phenotype linkage necessary for recovery of affinity selected sequences. The single-chain MS2 VLP therefore unites in a single structural platform the selective power of phage display with the high immunogenicity of VLPs.
Mutilation of RNA phage Qβ virus-like particles: from icosahedrons to rods
Febs Letters, 2000
Icosahedral virus-like particles (VLPs) of RNA phage QL L are stabilized by four disulfide bonds of cysteine residues 74 and 80 within the loop between L L-strands F and G (FG loop) of the monomeric subunits, which determine the five-fold and quasisix-fold symmetry contacts of the VLPs. In order to reduce the stability of QL L VLPs, we mutationally converted the amino acid stretch 76-ANGSCD-81 within the FG loop into the 76-VGGVEL-81 sequence. It led to production in Escherichia coli cells of aberrant rod-like QL L VLPs, along with normal icosahedral capsids. The length of the rod-like particles exceeded 4^30 times the diameter of icosahedral QL L VLPs. ß
Recombinant rna phage qβ capsid particles synthesized and self-assembled in escherichia coli
Gene, 1993
The Escherichia coli RNA phage Qp coat protein-encoding gene (C) was amplified from native Qp RNA using a reverse transcription-PCR technique. Gene C contains sequences coding for both the 133-amino acid (aa) QP coat protein (CP) and the 329-aa read-through protein (Al) consisting of CP and an additional 196-aa C-terminal sequence, separated from CP within the C gene by an opal (UGA) stop codon. Primers ensuring the natural environment for gene C, especially within the ribosome-binding site, and supplying C with unique restriction sites at both ends have been prepared. An amplified 1062-bp PCR fragment was positioned under the control of the strong E. coli trp promoter (I',,.,) within a pGEM-derived plasmid. The synthesis of gene C products was confirmed electrophoretically and immunologically. An immunodiffusion test with anti-Q0 phage antibodies and electron microscopy evaluation of the purified recombinant products showed that when expressed, the Qp C gene was responsible for high-level synthesis and correct self-assembly of QP CP monomers into capsids indistinguishable morphologically and immunologically from QP phage particles, which we plan to use as surface display vectors.
Structure and function of virion RNA polymerase of crAss-like phage
2020
CrAss-like phages are a recently described family-level group of viruses that includes the most abundant virus in the human gut1,2. Genomes of all crAss-like phages encode a large virion-packaged protein2,3 that contains a DFDxD sequence motif, which forms the catalytic site in cellular multisubunit RNA polymerases (RNAPs)4. Using Cellulophaga baltica crAss-like phage phi14:2 as a model system, we show that this protein is a novel DNA-dependent RNAP that is translocated into the host cell along with the phage DNA and transcribes early phage genes. We determined the crystal structure of this 2,180-residue enzyme in a self-inhibited, likely pre-virion-packaged state. This conformation is attained with the help of a Cleft-blocking domain that interacts with the active site motif and occupies the RNA-DNA hybrid binding grove. Structurally, phi14:2 RNAP is most similar to eukaryotic RNAPs involved in RNA interference5,6, although most of phi14:2 RNAP structure (nearly 1,600 residues) map...
Journal of Bacteriology, 2012
We have sequenced and characterized two R-plasmid-dependent single-stranded RNA bacteriophages (RPD ssRNA phages), C-1 and Hagl1. Phage C-1 requires a conjugative plasmid of the IncC group, while Hgal1 requires the IncH group. Both the adsorption rate constants and one-step growth curves are determined for both phages. We also empirically confirmed the lysis function of the predicted lysis genes. Genomic sequencing and phylogenetic analyses showed that both phages belong to the Levivirus group and are most closely related to another IncP-plasmid-dependent ssRNA phage, PRR1. Furthermore, our result strongly suggests that the stereotypical bauplans of genome organization found in Levivirus and Allolevivirus predate phage specialization for conjugative plasmids, suggesting that the utilization of conjugative plasmids for cell attachment and entry comprises independent evolutionary events for these two main clades of ssRNA phages. Our result is also consistent with findings of a previous study, making the Levivirus-like genome organization ancestral and the Allolevivirus-like genome derived. To obtain a deeper insight into the evolution of ssRNA phages, more phages specializing for various conjugative plasmids and infecting different bacterial species would be needed.
Chapter 11. Phage Vaccines and Phage Therapy
Nanoscience & Nanotechnology Series, 2011
The application of combinatorial approaches in conjunction with phage display techniques might be critical for development of vaccines against various infective and cancer diseases. Phage technique allows the generation of novel immunogens representing structural/molecular mimics of pathogen-derived immunodominant epitopes, or protein domains displayed on phages capable of inducing protective antibodies, or construction of novel vaccines based on incorporation of antigenic/genetic variability of pathogens or cancer cells in the context of phage particles. The diversity of applications and success of phage display are due to its simplicity and flexibility along with the possibilities of very cheap large-scale production of phage particles by recovering them from infected bacterial culture supernatants as nearly 100% homogenous preparations. Phages are easy to manage, they resist heat and many organic solvents, chemicals, or other stresses, and, importantly, phage particles are highly immunogenic and do not require adjuvant. Furthermore, phages do not require the cold chain (requirement to store vaccines at refrigerated or frozen temperatures), which equates to lower transport and storage costs. Considering these points, recombinant phages should be viewed as promising vaccine discovery tools and vaccine delivery vectors, and it is worth even considering the possibility of replacing the delivery systems of known vaccines currently in use with phage particles as vaccine carriers. The chapter outlines the current advances in phage vaccine development and analyses possible advances of phages as engineered immunogens.