Bacteriophage OP1, lytic for Xanthomonas oryzae pv. oryzae, changes its host range by duplication and deletion of the small domain in the deduced tail fiber gene

ABSTRACT Carotovoricin Er is a phage-tail-like bacteriocin produced byErwinia carotovora subsp. carotovorastrain Er, a causative agent for soft rot disease in plants. Here we studied binding and killing spectra of carotovoricin Er preparations for various strains of the bacterium (strains 645Ar, EC-2, N786, and P7) and found that the preparations contain two types of carotovoricin Er with different host specificities; carotovoricin Era possessing a tail fiber protein of 68 kDa killed strains 645Ar and EC-2, while carotovoricin Erb with a tail fiber protein of 76 kDa killed strains N786 and P7. The tail fiber proteins of 68 and 76 kDa had identical N-terminal amino acid sequences for at least 11 residues. A search of the carotovoricin Er region in the chromosome of strain Er indicated the occurrence of a DNA inversion system for the tail fiber protein consisting of (i) two 26-bp inverted repeats inside and downstream of the tail fiber gene that flank a 790-bp fragment and (ii) a putative DNA invertase gene with a 90-bp recombinational enhancer sequence. In fact, when a 1,400-bp region containing the 790-bp fragment was amplified by a PCR using the chromosomal DNA of strain Er as the template, both the forward and the reverse nucleotide sequences of the 790-bp fragment were detected. DNA inversion of the 790-bp fragment also occurred in Escherichia coli DH5α when two compatible plasmids carrying either the 790-bp fragment or the invertase gene were cotransformed into the bacterium. Furthermore, hybrid carotovoricin CGE possessing the tail fiber protein of 68 or 76 kDa exhibited a host range specificity corresponding to that of carotovoricin Era or Erb, respectively. Thus, a DNA inversion altered the C-terminal part of the tail fiber protein of carotovoricin Er, altering the host range specificity of the bacteriocin.

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Bacteriophage T4 Host Range is Expanded by Duplications of a Small Domain of the Tail Fiber Adhesin

Journal of Molecular Biology ◽

10.1006/jmbi.1996.0281 ◽

1996 ◽

Vol 258 (5) ◽

pp. 726-731 ◽

Cited By ~ 94

Author(s):

F. Tétart ◽

F. Repoila ◽

C. Monod ◽

H.M. Krisch

Keyword(s):

Host Range ◽

Bacteriophage T4 ◽

Tail Fiber ◽

Small Domain

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Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract

10.1101/2020.07.20.212829 ◽

2020 ◽

Author(s):

Sabrina I. Green ◽

Carmen Gu Liu ◽

Xue Yu ◽

Shelley Gibson ◽

Wilhem Salmen ◽

...

Keyword(s):

Gastrointestinal Tract ◽

Chemical Properties ◽

Protein Product ◽

Lytic Cycle ◽

Tail Fiber ◽

Bacterial Host ◽

Intestinal Mucus ◽

Mucosal Surfaces ◽

Epithelial Cell Surface ◽

Fiber Gene

AbstractThe human mucosal surface consists of a eukaryotic epithelium, a prokaryotic microbiota, and a carbohydrate-rich interface that separates them. Bacteriophage parasitize the prokaryotes but are not known to associate with eukaryotic cells. In the gastrointestinal tract, the interaction of these two domains influences the health of the host, especially colonization with invasive pathobionts. Antibiotics may be used but they also kill protective commensals and lack the physio-chemical properties to be specifically and optimally active in this complex milieu. Here, we report a novel phage whose lytic cycle is enhanced in intestinal environments. The enhanced activity is encoded in its tail fiber gene, whose protein product binds human heparan sulfated proteoglycans and localizes the phage to the epithelial cell surface, thereby positioning it near its bacterial host, a type of locational targeting mechanism. This finding offers the prospect of developing epithelial-targeting phage to selectively remove invasive pathobiont species from mucosal surfaces.Graphical AbstractModel showing (1) mucins from the intestinal mucus layer inhibit phage infection, (2) phage ES17 can bind to mucin and utilize other intestinal glycans as a receptor to infect and kill mucus-coated bacteria, and (3) phages like ES17 can be utilized to coat the intestinal epithelium by binding heparan sulfate glycans to protect from invasive pathogen infection.

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Host Range Expansion of Pseudomonas Virus LUZ7 Is Driven by a Conserved Tail Fiber Mutation

PHAGE ◽

10.1089/phage.2020.0006 ◽

2020 ◽

Vol 1 (2) ◽

pp. 87-90 ◽

Cited By ~ 2

Author(s):

Maarten Boon ◽

Dominique Holtappels ◽

Cédric Lood ◽

Vera van Noort ◽

Rob Lavigne

Keyword(s):

Host Range ◽

Range Expansion ◽

Tail Fiber ◽

Host Range Expansion

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Comparative Genomics of Streptococcus thermophilus Phage Species Supports a Modular Evolution Theory

Journal of Virology ◽

10.1128/jvi.73.10.8647-8656.1999 ◽

1999 ◽

Vol 73 (10) ◽

pp. 8647-8656 ◽

Cited By ~ 102

Author(s):

Sacha Lucchini ◽

Frank Desiere ◽

Harald Brüssow

Keyword(s):

Dna Recombination ◽

Point Mutations ◽

Streptococcus Thermophilus ◽

Tail Fiber ◽

Dna Repeats ◽

Modular Evolution ◽

Fiber Protein ◽

Variable Domains ◽

Replication Region ◽

Fiber Gene

ABSTRACT The comparative analysis of five completely sequencedStreptococcus thermophilus bacteriophage genomes demonstrated that their diversification was achieved by a combination of DNA recombination events and an accumulation of point mutations. The five phages included lytic and temperate phages, both pacsite and cos site, from three distinct geographical areas. The units of genetic exchange were either large, comprising the entire morphogenesis gene cluster, excluding the putative tail fiber genes, or small, consisting of one or maximally two genes or even segments of a gene. Many indels were flanked by DNA repeats. Differences in a single putative tail fiber gene correlated with the host ranges of the phages. The predicted tail fiber protein consisted of highly conserved domains containing conspicuous glycine repeats interspersed with highly variable domains. As in the T-even coliphage adhesins, the glycine-containing domains were recombinational hot spots. Downstream of a highly conserved DNA replication region, all lytic phages showed a short duplication; in three isolates the origin of replication was repeated. The lytic phages could conceivably be derived from the temperate phages by deletion and multiple rearrangement events in the lysogeny module, giving rise to occasional selfish phages that defy the superinfection control systems of the corresponding temperate phages.

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Genetic definition of two functional elements in a bacteriophage T4 host-range "cassette".

Genetics ◽

10.1093/genetics/122.3.471 ◽

1989 ◽

Vol 122 (3) ◽

pp. 471-479

Author(s):

M Snyder ◽

W B Wood

Keyword(s):

Host Range ◽

Bacteriophage T4 ◽

Temperature Sensitive ◽

Tail Fiber ◽

Neighboring Gene ◽

Distal Half ◽

Bacterial Surface ◽

Fiber Assembly ◽

Proximal Half ◽

Carboxy Terminal

Abstract Gene 37 of T4 encodes the major subunit of the distal half of the tail fiber. The distal tip of the fiber, comprised of the carboxy-terminal ends of two molecules of gene 37 product (gp37), carries the principal determinant of the phage host range. The gp37 carboxyl termini recognize the bacterial surface during infection, and, in addition, include a site required for interaction with the product of gp38 during distal half-fiber assembly. In the absence of interaction with gp38, gp37 polypeptides do not dimerize. Eleven temperature-sensitive mutants with defects located near the promoter-distal end of gene 37 were tested at nonpermissive temperatures for production of an antigen that is diagnostic of distal half-fiber assembly. Six of the mutations prevent distal half-fiber assembly. The other five allow assembly of distal half fibers, which combine with proximal half fibers and attach to phage particles, but the resulting phage do not adsorb to bacteria. These two classes of mutations define two adjacent but separate genetic regions, corresponding to two different functional domains in gp37. These two regions and the neighboring gene 38 comprise a functional unit that can be considered as a host-range "cassette," with features that are strikingly similar to corresponding functional units in other unrelated as well as related phages.

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A Tail Fiber Protein and a Receptor-Binding Protein Mediate ICP2 Bacteriophage Interactions with Vibrio cholerae OmpU

Journal of Bacteriology ◽

10.1128/jb.00141-21 ◽

2021 ◽

Author(s):

Andrea N.W. Lim ◽

Minmin Yen ◽

Kimberley D. Seed ◽

David W. Lazinski ◽

Andrew Camilli

Keyword(s):

Host Range ◽

Vibrio Cholerae ◽

Receptor Binding ◽

Mutant Phenotype ◽

Tail Fiber ◽

Missense Mutations ◽

Wild Type ◽

Mutant Strains ◽

Stool Samples ◽

Receptor Binding Protein

ICP2 is a virulent bacteriophage (phage) that preys on Vibrio cholerae. ICP2 was first isolated from cholera patient stool samples. Some of these stools also contained ICP2-resistant isogenic V. cholerae strains harboring missense mutations in the trimeric outer membrane porin protein OmpU, identifying it as the ICP2 receptor. In this study, we identify the ICP2 proteins that mediate interactions with OmpU by selecting for ICP2 host-range mutants within infant rabbits infected with a mixture of wild type and OmpU mutant strains. ICP2 host-range mutants, that can now infect OmpU mutant strains, had missense mutations in putative tail fiber gene gp25 and putative adhesin gp23. Using site-specific mutagenesis we show that single or double mutations in gp25 are sufficient to generate the host-range mutant phenotype. However, at least one additional mutation in gp23 is required for robust plaque formation on specific OmpU mutants. Mutations in gp23 alone were insufficient to give a host-range mutant phenotype. All ICP2 host-range mutants retained the ability to plaque on wild type V. cholerae cells. The strength of binding of host-range mutants to V. cholerae correlated with plaque morphology, indicating that the selected mutations in gp25 and gp23 restore molecular interactions with the receptor. We propose that ICP2 host-range mutants evolve by a two-step process where, first, gp25 mutations are selected for their broad host-range, albeit accompanied by low level phage adsorption. Subsequent selection occurs for gp23 mutations that further increase productive binding to specific OmpU alleles, allowing for near wild type efficiencies of adsorption and subsequent phage multiplication. Importance Concern over multidrug-resistant bacterial pathogens, including Vibrio cholerae, has led to a renewed interest in phage biology and their potential for phage therapy. ICP2 is a genetically unique virulent phage isolated from cholera patient stool samples. It is also one of three phages in a prophylactic cocktail shown to be effective in animal models of infection and the only one of the three that requires a protein receptor (OmpU). This study identifies an ICP2 tail fiber and a receptor binding protein and examines how ICP2 responds to the selective pressures of phage-resistant OmpU mutants. We found that this particular co-evolutionary arms race presents fitness costs to both ICP2 and V. cholerae.

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Engineering Phage Host-Range and Suppressing Bacterial Resistance Through Phage Tail Fiber Mutagenesis

10.1242/prelights.12577 ◽

2019 ◽

Author(s):

Zhang-He Goh

Keyword(s):

Host Range ◽

Bacterial Resistance ◽

Tail Fiber ◽

Phage Tail

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Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13

Viruses ◽

10.3390/v14010006 ◽

2021 ◽

Vol 14 (1) ◽

pp. 6

Author(s):

Olga Pacios ◽

Laura Fernández-García ◽

Inés Bleriot ◽

Lucia Blasco ◽

Antón Ambroa ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Host Range ◽

Burst Size ◽

Three Dimensional ◽

Genomic Analysis ◽

Amino Acid Sequences ◽

Phylogenetic Study ◽

Tail Fiber ◽

Homing Endonucleases ◽

Query Cover

Klebsiella pneumoniae is a human pathogen that worsens the prognosis of many immunocompromised patients. Here, we annotated and compared the genomes of two lytic phages that infect clinical strains of K. pneumoniae (vB_KpnM-VAC13 and vB_KpnM-VAC66) and phenotypically characterized vB_KpnM-VAC66 (time of adsorption of 12 min, burst size of 31.49 ± 0.61 PFU/infected cell, and a host range of 20.8% of the tested strains). Transmission electronic microscopy showed that vB_KpnM-VAC66 belongs to the Myoviridae family. The genomic analysis of the phage vB_KpnM-VAC66 revealed that its genome encoded 289 proteins. When compared to the genome of vB_KpnM-VAC13, they showed a nucleotide similarity of 97.56%, with a 93% of query cover, and the phylogenetic study performed with other Tevenvirinae phages showed a close common ancestor. However, there were 21 coding sequences which differed. Interestingly, the main differences were that vB_KpnM-VAC66 encoded 10 more homing endonucleases than vB_KpnM-VAC13, and that the nucleotidic and amino-acid sequences of the L-shaped tail fiber protein were highly dissimilar, leading to different three-dimensional protein predictions. Both phages differed significantly in their host range. These viruses may be useful in the development of alternative therapies to antibiotics or as a co-therapy increasing its antimicrobial potential, especially when addressing multidrug resistant (MDR) pathogens.

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Evaluating Phage Tail Fiber Receptor-Binding Proteins Using a Luminescent Flow-Through 96-Well Plate Assay

Frontiers in Microbiology ◽

10.3389/fmicb.2021.741304 ◽

2021 ◽

Vol 12 ◽

Author(s):

Emma L. Farquharson ◽

Ashlyn Lightbown ◽

Elsi Pulkkinen ◽

Téa Russell ◽

Brenda Werner ◽

...

Keyword(s):

Escherichia Coli ◽

Host Range ◽

Infection Process ◽

Bacterial Disease ◽

Tail Fiber ◽

Long Tail ◽

Bacterial Surface ◽

Specific Phage ◽

Phage Tail ◽

Tail Fibers

Phages have demonstrated significant potential as therapeutics in bacterial disease control and as diagnostics due to their targeted bacterial host range. Host range has typically been defined by plaque assays; an important technique for therapeutic development that relies on the ability of a phage to form a plaque upon a lawn of monoculture bacteria. Plaque assays cannot be used to evaluate a phage’s ability to recognize and adsorb to a bacterial strain of interest if the infection process is thwarted post-adsorption or is temporally delayed, and it cannot highlight which phages have the strongest adsorption characteristics. Other techniques, such as classic adsorption assays, are required to define a phage’s “adsorptive host range.” The issue shared amongst all adsorption assays, however, is that they rely on the use of a complete bacteriophage and thus inherently describe when all adsorption-specific machinery is working together to facilitate bacterial surface adsorption. These techniques cannot be used to examine individual interactions between a singular set of a phage’s adsorptive machinery (like long tail fibers, short tail fibers, tail spikes, etc.) and that protein’s targeted bacterial surface receptor. To address this gap in knowledge we have developed a high-throughput, filtration-based, bacterial binding assay that can evaluate the adsorptive capability of an individual set of a phage’s adsorption machinery. In this manuscript, we used a fusion protein comprised of an N-terminal bioluminescent tag translationally fused to T4’s long tail fiber binding tip (gp37) to evaluate and quantify gp37’s relative adsorptive strength against the Escherichia coli reference collection (ECOR) panel of 72 Escherichia coli isolates. Gp37 could adsorb to 61 of the 72 ECOR strains (85%) but coliphage T4 only formed plaques on 8 of the 72 strains (11%). Overlaying these two datasets, we were able to identify ECOR strains incompatible with T4 due to failed adsorption, and strains T4 can adsorb to but is thwarted in replication at a step post-adsorption. While this manuscript only demonstrates our assay’s ability to characterize adsorptive capabilities of phage tail fibers, our assay could feasibly be modified to evaluate other adsorption-specific phage proteins.

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