Genome-scale top-down reduction of phages to generate viable minimal phage genomes

Reduction of tailed-phage genomes to generate viable minimal genome phages is important for expanding our understanding of phage biology, providing insights for phage synthetic biology. Many efforts have been made to minimize living cells, but such work remains a challenge for phages due to the extraordinary genomic diversity and lack of genome-scale editing techniques. Here, we developed a CRISPR/Cas9-based iterative phage genome reduction (CiPGr) approach to detect the nonessential gene set of phages and minimize phage genomes. By CiPGr, inactivated genes accumulated on the phage genome, and mutant progeny with robust growth gradually arose, eventually becoming predominant in the populations. CiPGr was applied to four distinct tailed phages (model phages T7 and T4; wild-type phages seszw and selz), resulting in mutants of these phages with deletion of 8–20% (3.3–33 kbp) sequences, and leading to minimal genomes. Metagenomic sequencing of the mutant phage populations generated showed that 46.7 to 65.4% of genes of these phages were removed. Loss of some genes (39.6%-50%) in the removable gene sets was likely severely detrimental to phage growth. This made the corresponding mutant progenies recede in the populations, leading to the failure of detection of these genes in the genomes of the isolated mutants. In summary, our results for these four distinct tailed phages demonstrated that CiPGr is a generic yet effective approach suitable for use in novel phages without prior knowledge.

A mutant bacteriophage evolved to infect resistant bacteria gained a broader host range

SummaryBacteriophages (phages) are the most abundant entities in nature, yet little is known about their capacity to acquire new hosts and invade new niches. By exploiting the Gram positive soil bacteriumBacillus subtilis(B. subtilis) and its lytic phage SPO1 as a model, we followed the co-evolution of bacteria and phages. After infection, phage resistant bacteria were readily isolated. These bacteria were defective in production of glycosylated wall teichoic acid (TA) polymers, served as SPO1 receptor. Subsequently, a SPO1 mutant phage that could infect the resistant bacteria evolved. The emerging phage contained mutations in two genes, encoding the baseplate and fibers required for host attachment. Remarkably, the mutant phage gained the capacity to infect non-hostBacillusspecies that are not infected by the wild type phage. We provide evidence that the evolved phage lost its dependency on the species specific glycosylation pattern of TA polymers. Instead, the mutant phage gained the capacity to directly adhere to the TA backbone, conserved among different species, thereby crossing the species barrier.

Computational modeling of bacteriophage self-assembly during formation of hierarchical structures

ABSTRACTDesigning new materials with well-defined structures and desired functions is a challenge in materials science, especially with nanomaterials. Nature, however, solves design of these materials through a self-assembling, hierarchically ordered process. We have investigated the mechanisms by which the high- aspect ratio and unique surface chemistry of M13 bacteriophage can give rise to increasingly complex, hierarchically ordered, bundled phage structures with a wide range of material applications. A molecular dynamic simulation of the 3-D structure of a 20-nm section of wild type (WT) and mutant phage types were developed based on WT phage crystal structure and ab initio calculations. Simulations of these phage were then used to examine repulsive and attractive forces of the particles in solution. Examination of contact interactions between two WT phage indicated the phage were maximally attracted to each other in a head to tail orientation. A mutant phage (4E) with a higher negative surface charge relative to WT phage also preferentially ordered head to tail in solution. In contrast, a mutant phage (CLP8) with a net positive surface charge had minimal repulsion in a 90° orientation. Understanding the self-assembly process through molecular dynamic simulations and decomposition of fundamental forces driving inter- and intra-strand interactions has provided a qualitative assessment of mechanisms that lead to hierarchical phage bundle structures. Results from simulation agree with experimentally observed patterns from self-assembly. We anticipate using this system to further investigate development of hierarchical structures not only from biological molecules but also from synthetic materials.

Molecular Characterization of a Variant of Bacillus anthracis-Specific Phage AP50 with Improved Bacteriolytic Activity

ABSTRACT The genome sequence of a Bacillus anthracis-specific clear plaque mutant phage, AP50c, contains 31 open reading frames spanning 14,398 bp, has two mutations compared to wild-type AP50t, and has a colinear genome architecture highly similar to that of gram-positive Tectiviridae phages. Spontaneous AP50c-resistant B. anthracis mutants exhibit a mucoid colony phenotype.

H-mutant Bacteriophages as a Potential Biocontrol of Bacterial Blight of Geranium

Bacteriophages specific to Xanthomonas campestris pv. pelargonii (Xcp), the causal agent of bacterial blight of geranium, Pelargonium ×hortorum L.H. Bailey, were isolated from soil and sludge samples from Florida, California, Minnesota, and Utah. Sixteen phages were evaluated for their potential to lyse 21 Xcp strains collected from around the world. The Xcp strains varied in their susceptibility to the phage isolates with 4 to 14 phages producing a lytic or highly virulent reaction. A mixture of five h-mutants was developed from phages that exhibited the broadest host-ranges and tested against the same Xcp strains. The h-mutant phage mixture lysed all 21 Xcp strains. Three experiments were designed to determine the efficacy of using a mixture of four h-mutant phages to control the spread of the bacterial blight pathogen on potted and seedling geraniums under greenhouse conditions. Plants surrounding diseased inoculated plants were treated with a phage mixture at 5 × 108 pfu/mL daily, biweekly, or triweekly, or treated with Phyton-27®, at 2.0 mL·L-1 every 10 or 14 days. In potted geraniums, daily foliar sprays of the phage mixture had reduced disease incidence and severity by 50% and 75%, respectively, relative to control plants after 6 weeks. In two plug experiments, the phage mixture applied daily also had reduced disease incidence and severity by 69% and 86%, and 85% and 92%, respectively, when compared with controls after 5 weeks. In all three experiments, disease incidence and severity were less for plants treated daily with phages than for those treated less frequently with phages or with Phyton-27®. Chemical name used: copper sulfate pentahydrate (Phyton-27®).

The quantification of protein bioactivity, Phage T4 lysozymes substituted at residue 86

Data taken from the literature for the activity of mutant Phage T4 lysozymes substituted at residue 86 were correlated with the intermolecular force (IMF) equation with very good results. The activity determined was the relative amount of enzyme required to give a cleared area with a radius of 7.00 mm in the lysoplate assay of Becktel and Baase. The best regression equation obtained shows hydrogen bonding to be the major factor in determining activity, with dispersion forces next in importance and steric effects least. No dependence on side chain charge was observed. The results support the utility of the IMF equation as a quantitative model of protein bioactivity.