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PreprintCited by 25Bacteriophages and microbial interactionsAdvanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and Function

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Structure and host specificity of Staphylococcus epidermidis bacteriophage Andhra

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Hawkins, N’Toia C., Kizziah, James L., Hatoum-Aslan, Asma, Dokland, Terje·2022·Science Advances
DOI 10.1101/2022.07.21.500982PMC PMC9710869

Preprint — published as 10.1126/sciadv.ade0459 · Paper page

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Abstract

Staphylococcus epidermidis is an opportunistic pathogen of the human skin, often associated with infections of implanted medical devices. An increase in antibiotic resistance in S. epidermidis and other bacterial pathogens has led to renewed interest in the use of bacteriophages as an alternative to conventional antibiotics. Staphylococcal picoviruses are a group of strictly lytic, short-tailed bacteriophages with compact genomes that are attractive candidates for therapeutic use. Here, we report the structure of the complete virion of S. epidermidis -infecting phage Andhra, determined using high-resolution cryo-electron microscopy, allowing atomic modeling of the capsid and tail proteins, including twelve trimers of a unique receptor binding protein, the hexameric tail knob that acts as a gatekeeper for DNA ejection, and the tail tip, which is a heterooctamer of two different lytic proteins. Our findings elucidate critical features that enable host recognition and penetration, facilitating the development of this group of phages for therapeutic applications.

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Figures

Fig. 1. Comparison of Andhra, P68, and ϕ29 genomes. ORFs are numbered in each genome, and relevant genes are labeled. Genes encoding structural proteins are color coded: Tail tip protein (Tip), brown; RBP anchor (Anc), dark blue; terminal protein (5TP), light green; tail tip lysin (LysT), gray; tail knob protein (Knob), cyan; head fiber (Fib), salmon; RBP, gold; tail stem/collar protein (Stem), green; portal protein (PP), magenta; major capsid protein (CP), blue; capsid lining protein (CLP), yellow; core (Cor)/scaffolding (SP) protein, red. Nonstructural proteins include the packaging ATPase (Pac), hatched; the DNA polymerase (Pol), black; and the single-stranded DNA binding protein (SDB), holin (Hol) and endolysin (Lys), white. The stippled areas between the Andhra and P68 genomes indicate regions of >70% nucleotide identity, calculated in BLASTN (29). The ϕ29 genome was split between ORFs 7 and 6, and the right end was moved to the left side (indicated by the duplicated ORFs in gray) to facilitate a more direct comparison to Andhra and P68.
Fig. 1. Comparison of Andhra, P68, and ϕ29 genomes. ORFs are numbered in each genome, and relevant genes are labeled. Genes encoding structural proteins are color coded: Tail tip protein (Tip), brown; RBP anchor (Anc), dark blue; terminal protein (5TP), light green; tail tip lysin (LysT), gray; tail knob protein (Knob), cyan; head fiber (Fib), salmon; RBP, gold; tail stem/collar protein (Stem), green; portal protein (PP), magenta; major capsid protein (CP), blue; capsid lining protein (CLP), yellow; core (Cor)/scaffolding (SP) protein, red. Nonstructural proteins include the packaging ATPase (Pac), hatched; the DNA polymerase (Pol), black; and the single-stranded DNA binding protein (SDB), holin (Hol) and endolysin (Lys), white. The stippled areas between the Andhra and P68 genomes indicate regions of >70% nucleotide identity, calculated in BLASTN (29). The ϕ29 genome was split between ORFs 7 and 6, and the right end was moved to the left side (indicated by the duplicated ORFs in gray) to facilitate a more direct comparison to Andhra and P68.CC BY · PubMed Central
Fig. 2. Isosurface representations of the reconstructions. (A) Asymmetric reconstruction of the whole virion, colored radially from the center of the capsid according to the color bar (distances in angstrom). Rendered at 5 SDs above the mean (5σ). The tail tip was not visible in the reconstruction at this cutoff and is indicated by the outline. (B) The asymmetric reconstruction viewed from the bottom (tail end), showing the sixfold symmetric arrangement of the appendages. (C) A 50-Å-thick slab through the asymmetric reconstruction, showing the concentric rings of DNA in the interior and the DNA inside the tail (arrow). Colored radially from the center of the capsid according to the color bar. (D) Icosahedral reconstruction of the capsid, rendered at 3σ and colored radially from the capsid center according to the color bar. The asymmetric unit triangle is shown, with fivefold, threefold, and twofold symmetry axes denoted by the pentagon, triangles, and oval, respectively. (E) C6 reconstruction of the tail, rendered at 3σ and colored radially from the central axis according to the color bar. The tail tip is indicated by the outline. (F) Cutaway view of the tail, rendered and colored as in (E). (G) Focused C6 reconstruction of the distal tail, showing the tail knob, rendered at 6σ and colored as in (E). (H) Focused asymmetric reconstruction of the tail tip, rendered at 2.5σ and colored radially from the central axis according to the color bar.
Fig. 2. Isosurface representations of the reconstructions. (A) Asymmetric reconstruction of the whole virion, colored radially from the center of the capsid according to the color bar (distances in angstrom). Rendered at 5 SDs above the mean (5σ). The tail tip was not visible in the reconstruction at this cutoff and is indicated by the outline. (B) The asymmetric reconstruction viewed from the bottom (tail end), showing the sixfold symmetric arrangement of the appendages. (C) A 50-Å-thick slab through the asymmetric reconstruction, showing the concentric rings of DNA in the interior and the DNA inside the tail (arrow). Colored radially from the center of the capsid according to the color bar. (D) Icosahedral reconstruction of the capsid, rendered at 3σ and colored radially from the capsid center according to the color bar. The asymmetric unit triangle is shown, with fivefold, threefold, and twofold symmetry axes denoted by the pentagon, triangles, and oval, respectively. (E) C6 reconstruction of the tail, rendered at 3σ and colored radially from the central axis according to the color bar. The tail tip is indicated by the outline. (F) Cutaway view of the tail, rendered and colored as in (E). (G) Focused C6 reconstruction of the distal tail, showing the tail knob, rendered at 6σ and colored as in (E). (H) Focused asymmetric reconstruction of the tail tip, rendered at 2.5σ and colored radially from the central axis according to the color bar.CC BY · PubMed Central
Fig. 3. The capsid. (A) Ribbon diagram of the entire icosahedral capsid, viewed down a twofold axis, as in Fig. 2D. CP subunits are color coded: A, red; B, blue; C, green; D, yellow. An asymmetric unit triangle, delimited by fivefold, twofold, and two threefold axes, is shown. (B) Ribbon diagram showing one hexamer and one pentamer, viewed from the outside of the capsid. The four CP subunits in one asymmetric unit are colored as in (A). The corresponding CLP (gp19) subunits are color coded: E, pink; F, purple; G, light green; H, orange. (C) Ribbon diagram of CP subunit B, colored by domain: N-arm, red; E-loop, yellow; P-domain, green; A-domain, blue; insertion domain, cyan. The corresponding CLP (subunit F) is purple. The bottom panel is rotated 90°. Pertinent residues are numbered. (D) One asymmetric unit, viewed from the inside of the capsid, showing the CLPs, colored as in (B) with atoms represented as spheres. CP is shown as a gray molecular surface. (E) Ribbon diagram of the head fiber (gp13) trimer model (scarlet, ruby, and crimson), showing its attachment to the CP hexamer. Capsid density is shown as a transparent gray isosurface, with the corresponding CP subunit models inside. (F) Ribbon diagram of the head fiber trimer fitted into the asymmetric reconstruction density (transparent surface), viewed perpendicularly to the axis of the fiber and numbered by residue.
Fig. 3. The capsid. (A) Ribbon diagram of the entire icosahedral capsid, viewed down a twofold axis, as in Fig. 2D. CP subunits are color coded: A, red; B, blue; C, green; D, yellow. An asymmetric unit triangle, delimited by fivefold, twofold, and two threefold axes, is shown. (B) Ribbon diagram showing one hexamer and one pentamer, viewed from the outside of the capsid. The four CP subunits in one asymmetric unit are colored as in (A). The corresponding CLP (gp19) subunits are color coded: E, pink; F, purple; G, light green; H, orange. (C) Ribbon diagram of CP subunit B, colored by domain: N-arm, red; E-loop, yellow; P-domain, green; A-domain, blue; insertion domain, cyan. The corresponding CLP (subunit F) is purple. The bottom panel is rotated 90°. Pertinent residues are numbered. (D) One asymmetric unit, viewed from the inside of the capsid, showing the CLPs, colored as in (B) with atoms represented as spheres. CP is shown as a gray molecular surface. (E) Ribbon diagram of the head fiber (gp13) trimer model (scarlet, ruby, and crimson), showing its attachment to the CP hexamer. Capsid density is shown as a transparent gray isosurface, with the corresponding CP subunit models inside. (F) Ribbon diagram of the head fiber trimer fitted into the asymmetric reconstruction density (transparent surface), viewed perpendicularly to the axis of the fiber and numbered by residue.CC BY · PubMed Central
Fig. 4. The tail structure. (A) Ribbon diagram of the composite model of the Andhra tail proteins, viewed from the side and colored as in Fig. 1: core protein (gp20), red; PP (gp17), magenta; tail stem protein (gp16), green; RBP (gp15), gold; RBP anchor (gp6), blue; tail knob protein (gp12), cyan; tail tip lysin (gp10), gray; tail tip protein (gp1), brown. (B) Model of the tail, viewed from the bottom; knob and tip not included. (C) One asymmetric unit of the C6 tail reconstruction, comprising 12 copies of core protein (gp20), two copies of PP (gp17), two copies of tail stem protein (gp16), six copies (two trimers) of RBP (gp15), and two copies of the anchor protein (gp6). (Knob and tip not included.) The connections between the N- and C-terminal domains of gp6 are indicated by the dotted lines. (D) PP monomer with the wing, stem, and clip domains colored blue, green, and purple, respectively. The corresponding six copies of the core protein (gp20) are shown in red. (E) One RBP trimer, with protomers colored blue, green, and purple. The N and C termini are indicated. (F) Ribbon diagram of a section through the tail, viewed from the bottom, showing a dimer of gp6 (blue and purple) interacting with the barrel of the tail stem (green) and the RBPs (gold). (G) A 90° rotated view of the gp6 dimer, viewed perpendicular to the axis of the tail. N and C termini are indicated. Pertinent residues are numbered in (C) to (E) and (G).
Fig. 4. The tail structure. (A) Ribbon diagram of the composite model of the Andhra tail proteins, viewed from the side and colored as in Fig. 1: core protein (gp20), red; PP (gp17), magenta; tail stem protein (gp16), green; RBP (gp15), gold; RBP anchor (gp6), blue; tail knob protein (gp12), cyan; tail tip lysin (gp10), gray; tail tip protein (gp1), brown. (B) Model of the tail, viewed from the bottom; knob and tip not included. (C) One asymmetric unit of the C6 tail reconstruction, comprising 12 copies of core protein (gp20), two copies of PP (gp17), two copies of tail stem protein (gp16), six copies (two trimers) of RBP (gp15), and two copies of the anchor protein (gp6). (Knob and tip not included.) The connections between the N- and C-terminal domains of gp6 are indicated by the dotted lines. (D) PP monomer with the wing, stem, and clip domains colored blue, green, and purple, respectively. The corresponding six copies of the core protein (gp20) are shown in red. (E) One RBP trimer, with protomers colored blue, green, and purple. The N and C termini are indicated. (F) Ribbon diagram of a section through the tail, viewed from the bottom, showing a dimer of gp6 (blue and purple) interacting with the barrel of the tail stem (green) and the RBPs (gold). (G) A 90° rotated view of the gp6 dimer, viewed perpendicular to the axis of the tail. N and C termini are indicated. Pertinent residues are numbered in (C) to (E) and (G).CC BY · PubMed Central
Fig. 5. Distal tail structure. (A) Ribbon diagram of the tail knob (gp12) hexamer. One protomer is colored cyan. Tail stem (g16) loops are in red. (B) gp12 hexamer, viewed from the tail tip. Each protomer is colored in a different shade. (C) Ribbon diagram of a gp12 monomer: N-terminal domain, blue; N-to-C linker, cyan; tip domain, green; channel loop, yellow; C-terminal domain, red. Pertinent residues are numbered. (D) Isosurface (2.5σ) of the focused asymmetric reconstruction of the tail tip with gp10 and gp1 shown in blue and gold, respectively. (E) Ribbon diagram showing the two subunits of gp10 (red and blue). The N-terminal GyH, middle linker, and C-terminal CHAP domains are labeled, the flexible linkers are indicated by dashed lines, and the twofold symmetry axis is indicated by the filled oval. (F) Ribbon diagram showing the six subunits of gp1 in the tail tip arranged as three dimers, colored brown, sand, and gold. The twofold symmetry axis is indicated by the filled oval; peripheral dimer twofold axes are shown as open ovals. N and C termini are indicated on one dimer. (G) Ribbon diagram of the tail tip model, showing gp10 and gp1, colored as in (E) and (F) and viewed as in (E). (H) A 15-Å-thick slab through the asymmetric virion reconstruction, showing the central density in the tail with double stranded DNA and the gp7 model (orange) fitted in. (I) Left: Ribbon diagram of the AlphaFold model for gp7 (green). Middle: The modified gp7 model (pink) superimposed on the ϕ29 gp3 crystal structure (blue). Right: gp7 (salmon) modified to fit into the central tail density. N and C termini are indicated, and the serine residues near the top of the molecule (S123, S127, and S132) are shown as red spheres.
Fig. 5. Distal tail structure. (A) Ribbon diagram of the tail knob (gp12) hexamer. One protomer is colored cyan. Tail stem (g16) loops are in red. (B) gp12 hexamer, viewed from the tail tip. Each protomer is colored in a different shade. (C) Ribbon diagram of a gp12 monomer: N-terminal domain, blue; N-to-C linker, cyan; tip domain, green; channel loop, yellow; C-terminal domain, red. Pertinent residues are numbered. (D) Isosurface (2.5σ) of the focused asymmetric reconstruction of the tail tip with gp10 and gp1 shown in blue and gold, respectively. (E) Ribbon diagram showing the two subunits of gp10 (red and blue). The N-terminal GyH, middle linker, and C-terminal CHAP domains are labeled, the flexible linkers are indicated by dashed lines, and the twofold symmetry axis is indicated by the filled oval. (F) Ribbon diagram showing the six subunits of gp1 in the tail tip arranged as three dimers, colored brown, sand, and gold. The twofold symmetry axis is indicated by the filled oval; peripheral dimer twofold axes are shown as open ovals. N and C termini are indicated on one dimer. (G) Ribbon diagram of the tail tip model, showing gp10 and gp1, colored as in (E) and (F) and viewed as in (E). (H) A 15-Å-thick slab through the asymmetric virion reconstruction, showing the central density in the tail with double stranded DNA and the gp7 model (orange) fitted in. (I) Left: Ribbon diagram of the AlphaFold model for gp7 (green). Middle: The modified gp7 model (pink) superimposed on the ϕ29 gp3 crystal structure (blue). Right: gp7 (salmon) modified to fit into the central tail density. N and C termini are indicated, and the serine residues near the top of the molecule (S123, S127, and S132) are shown as red spheres.CC BY · PubMed Central

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Metadata

Authors
Hawkins, N. C., Kizziah, J. L., Hatoum-Aslan, A., & Dokland, T.
Affiliations
  • University of Alabama at Birmingham (US)
  • University of Illinois Urbana-Champaign (US)
Corresponding author
Dokland, Terje
ORCID
Venue
Science Advances
Publisher
openRxiv
Published
2022-07-21
Volume
8
Issue
48
Pages
eade0459-eade0459
ISSN
2375-2548 (ISSN-L)
DOI
10.1101/2022.07.21.500982
PMC
PMC9710869
OpenAlex
W4310437436
Cited by
25
References
1
Citations by year
2026: 6 · 2025: 7 · 2024: 7 · 2023: 5
FWCI
2.53
Type
journal article
Language
en
Open access
Locations
  • Science Advances (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • National Institute of General Medical Sciences (U24GM116789)
  • National Institute of Allergy and Infectious Diseases (R21AI156636, R01AI083255)
Topics
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
Staphylococcus epidermidis, phage structure, viral assembly, capsid, receptor binding protein, lytic proteins, host specificity, host recognition, DNA ejection, AlphaFold structure prediction, cryo-electron microscopy
MeSH terms
Capsid, Humans, Staphylococcus Phages, Staphylococcus epidermidis, Cryoelectron Microscopy, Capsid Proteins, Host Specificity

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