Structure of the Three N-Terminal Immunoglobulin Domains of the Highly Immunogenic Outer Capsid Protein from a T4-Like Bacteriophage

Fokine, Andrei; Islam, Mohammad Zahidul; Zhang, Zhihong; Bowman, Valorie D.; Rao, Venigalla B.; Rossmann, Michael G.

doi:10.1128/jvi.00847-11

Cited by 65 publications

(118 citation statements)

References 49 publications

Supporting

Mentioning

108

Contrasting

Unclassified

Order By: Relevance

“…The phages included a mucus-adherent T4 phage (T4) and a T4 Hoc deletion mutant (T4Δhoc). T4Δhoc does not have the Hoc protein exposed on its capsid and does not adhere to mucus, but is otherwise a normal, infective T4 phage (15). To assay for antibacterial activity of the phages in the mucus layer, we perfused chips with media containing T4 phage (10 7 mL -1 ), T4Δhoc phage (10 7 mL -1 ), or no phage for 24 h to saturate the mucosal epithelium.…”

Section: Resultsmentioning

confidence: 99%

“…E. coli B strain HER 1024 was used for all experiments and was grown in LB (10 g tryptone, 5 g yeast extract, 10 g NaCl, in 1 L dH 2 0) at 37°C overnight with shaking. The T4 Hoc phage deletion mutant (T4Δhoc) was kindly supplied by Venigalla B. Rao (The Catholic University of America, Washington, D.C.) (15). The human tumorigenic lung epithelial cell line A549 was obtained from the American Type Culture Collection and cultured in F12-K media with 10% FBS and 100 μg·mL -1 penicillin-streptomycin.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters

Barr

Auro

Sam-Soon

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

176

186

View full text Add to dashboard Cite

Bacteriophages (phages) defend mucosal surfaces against bacterial infections. However, their complex interactions with their bacterial hosts and with the mucus-covered epithelium remain mostly unexplored. Our previous work demonstrated that T4 phage with Hoc proteins exposed on their capsid adhered to mucin glycoproteins and protected mucus-producing tissue culture cells in vitro. On this basis, we proposed our bacteriophage adherence to mucus (BAM) model of immunity. Here, to test this model, we developed a microfluidic device (chip) that emulates a mucosal surface experiencing constant fluid flow and mucin secretion dynamics. Using mucus-producing human cells and Escherichia coli in the chip, we observed similar accumulation and persistence of mucus-adherent T4 phage and nonadherent T4Δhoc phage in the mucus. Nevertheless, T4 phage reduced bacterial colonization of the epithelium >4,000-fold compared with T4Δhoc phage. This suggests that phage adherence to mucus increases encounters with bacterial hosts by some other mechanism. Phages are traditionally thought to be completely dependent on normal diffusion, driven by random Brownian motion, for host contact. We demonstrated that T4 phage particles displayed subdiffusive motion in mucus, whereas T4Δhoc particles displayed normal diffusion. Experiments and modeling indicate that subdiffusive motion increases phage-host encounters when bacterial concentration is low. By concentrating phages in an optimal mucus zone, subdiffusion increases their host encounters and antimicrobial action. Our revised BAM model proposes that the fundamental mechanism of mucosal immunity is subdiffusion resulting from adherence to mucus. These findings suggest intriguing possibilities for engineering phages to manipulate and personalize the mucosal microbiome.BAM | virus | mucus | subdiffusion | search strategy I n all animals, mucosal surfaces provide critical immunological services by both protecting against invading bacterial pathogens and supporting large communities of commensal microorganisms (1, 2). Being exposed to the environment, mucosal surfaces are also the infection sites for many important bacterial diseases, including acute diarrhea and cystic fibrosis in humans. This, combined with their accessibility, make mucosal surfaces attractive venues for phage therapy; that is, the use of bacteriophages (phages) to treat and clear bacterial infections (3,4). Clinical success so far has been erratic (5). The complexities and dynamics of the mucus layer are rarely considered, and the activity of phages therein is mostly unknown. Not surprisingly, phages effective in vitro do not consistently reduce mucosal bacterial host levels in vivo (6, 7). An understanding of the interactions between phages and their bacterial hosts within the relevant physiological environment is critical for consistent success of phage therapy applications.The multilayered mucus is composed primarily of gel-forming mucin glycoproteins that are continually secreted by the underlying epithelium (8). The mucin...

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters

Barr

Auro

Sam-Soon

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

176

186

View full text Add to dashboard Cite

show abstract

“…Hoc decorates T4 heads by binding to sixfold symmetric vertices in hexameric capsomeres, thereby providing a polyvalent binding moiety on the outside of phage heads. Hoc is proposed to mediate binding of T4 to surfaces such as the Escherichia coli host cell (22), and has also been used for phage display to create new binding specificities for biotechnology applications (23). If the Ig-superfamily proteins studied here are also accessory head proteins, they may mediate binding of viral particles to candidate host cells or environmental materials, allowing selection to enrich for those binding specificities that optimize reproductive success.…”

Section: Discussionmentioning

confidence: 99%

Hypervariable loci in the human gut virome

Minot

Grunberg

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

180

184

View full text Add to dashboard Cite

Genetic variation is critical in microbial immune evasion and drug resistance, but variation has rarely been studied in complex heterogeneous communities such as the human microbiome. To begin to study natural variation, we analyzed DNA viruses present in the lower gastrointestinal tract of 12 human volunteers by determining 48 billion bases of viral DNA sequence. Viral genomes mostly showed low variation, but 51 loci of ∼100 bp showed extremely high variation, so that up to 96% of the viral genomes encoded unique amino acid sequences. Some hotspots of hypervariation were in genes homologous to the bacteriophage BPP-1 viral tail-fiber gene, which is known to be hypermutagenized by a unique reverse-transcriptase (RT)-based mechanism. Unexpectedly, other hypervariable loci in our data were in previously undescribed gene types, including genes encoding predicted Ig-superfamily proteins. Most of the hypervariable loci were linked to genes encoding RTs of a single clade, which we find is the most abundant clade among gut viruses but only a minor component of bacterial RT populations. Hypervariation was targeted to 5′-AAY-3′ asparagine codons, which allows maximal chemical diversification of the encoded amino acids while avoiding formation of stop codons. These findings document widespread targeted hypervariation in the human gut virome, identify previously undescribed types of genes targeted for hypervariation, clarify association with RT gene clades, and motivate studies of hypervariation in the full human microbiome.deep sequencing | diversity-generating retroelement | mutagenesis | major tropism determinant K ey aspects of host-parasite interactions are mediated by targeted changes in DNA. The vertebrate adaptive immune system is based on covalent DNA rearrangements that diversify genes encoding Ig-domain antigen-binding proteins. In response, viral and cellular pathogens encode genetic systems that vary antigens bound by host antigen receptors (1, 2).In this study we begin to characterize patterns of sequence variation in heterogeneous natural communities, using the human microbiome as a model. We chose to study viral samples because they represent a medically important microbiome component, but contain a smaller aggregate genome size than the full microbiome, allowing sequencing to a depth that permits empirical assessment of variation.A newly discovered mechanism of targeted hypermutation, particularly pertinent here, involves the Bordetella bacteriophage BPP-1, which has been shown to vary the sequence of the gene encoding its phage tail fiber to bind divergent cell-surface receptors (3-6). The phage-encoded major tropism determinant (MTD) gene, which encodes the tip of the tail fiber, is subjected to targeted hypermutation by a reverse transcriptase (RT)-dependent mechanism (7,8). The 3′ part of the tail-fiber gene is duplicated in the phage genome, and the duplicated template repeat (TR) is transcribed and reverse-transcribed in an error-prone fashion. The mutated copy is then incorporated into the MTD gene ...

show abstract

“…74 Each Hoc molecule contains 4 domains, 3 of which have immunoglobulin-like folds. [97][98][99] Immunoglobulin domains are present on the surfaces of ~25% of Caudovirales 100,101 indicating that these are beneficial for the phage life cycle. The presence of a large number of immunoglobulin domains probably makes the virion surface "sticky" and help the phage to bind reversibly to different surfaces.…”

mentioning

confidence: 99%