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Cited by 11Bacteriophages and microbial interactionsAntimicrobial Resistance in StaphylococcusEnzyme Structure and Function

The DOI matches its Crossref record; 65 of the 65 references it cites were found in a registry or an index.

Structure of the Staphylococcus aureus bacteriophage 80α neck shows details of the DNA, tail completion protein, and tape measure protein

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Kizziah, James L., Mukherjee, Amarshi, Parker, Laura K., Dokland, Terje·2025·Structure
DOI 10.1016/j.str.2025.03.007PMC PMC11661146

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Abstract

The Staphylococcus aureus pathogenicity islands (SaPIs), including SaPI1, are a type of mobile genetic elements (MGEs) that are mobilized at high frequency by "helper" bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from helper-encoded structural proteins. 80α and SaPI1 virions consist of an icosahedral head connected via a portal vertex to a long, non-contractile tail. A connector or "neck" forms the interface between the tail and the head. Here, we have determined the high-resolution structure of the neck section of SaPI1 virions, including the dodecameric portal and head-tail-connector proteins, and the hexameric head-tail joining, tail terminator and major tail proteins. We also resolved the DNA, the tail completion protein (TCP), and the tape measure protein (TMP) inside the tail, features that have not previously been observed at high resolution. Our study provides insights into the assembly and infection process in this important group of MGEs.

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Figures

Figure 1. Structure of the SaPI1 neck. (A) Schematic diagram of part of the late operon of 80α, showing the genes encoding neck proteins. ORF numbers and protein names are shown: TerS, small terminase subunit; TerL, large terminase subunit; PP, portal protein; EP, ejection protein, SP, scaffolding protein; CP, major capsid protein; HTCP, head-tail connector protein; HTJP, head-tail joining protein; TCP, tail completion protein; TrP, tail terminator protein; MTP, major tail protein; TMP, tape measure protein. The schematic diagram indicates the location of the neck proteins in the virion. The DNA is shown as a purple double helix. (B) Cryo-electron micrograph of SaPI1 virions. Scale bar = 50 nm. (C) Isosurface representation of a composite of the C6 neck reconstruction, colored by radius from the central axis, and the previously determined C12 reconstruction of the portal (gray) [30]. (D) Cutaway view of the asymmetric (C1) reconstruction of the neck, showing the DNA, TCP and TMP inside the neck, colored by radius according to the color bar. (E) Segmented reconstruction, colored by protein as in panel A: PP (gp42), gray; HTCP (gp49), blue; HTJP (gp50), green; TrP (gp52), pink; MTP (gp53), yellow. (F) Cutaway view of segmented reconstruction, showing density inside neck, colored as in panel C. In addition, the DNA is purple; TCP (gp51), orange; TMP (gp56), brown.
Figure 1. Structure of the SaPI1 neck. (A) Schematic diagram of part of the late operon of 80α, showing the genes encoding neck proteins. ORF numbers and protein names are shown: TerS, small terminase subunit; TerL, large terminase subunit; PP, portal protein; EP, ejection protein, SP, scaffolding protein; CP, major capsid protein; HTCP, head-tail connector protein; HTJP, head-tail joining protein; TCP, tail completion protein; TrP, tail terminator protein; MTP, major tail protein; TMP, tape measure protein. The schematic diagram indicates the location of the neck proteins in the virion. The DNA is shown as a purple double helix. (B) Cryo-electron micrograph of SaPI1 virions. Scale bar = 50 nm. (C) Isosurface representation of a composite of the C6 neck reconstruction, colored by radius from the central axis, and the previously determined C12 reconstruction of the portal (gray) [30]. (D) Cutaway view of the asymmetric (C1) reconstruction of the neck, showing the DNA, TCP and TMP inside the neck, colored by radius according to the color bar. (E) Segmented reconstruction, colored by protein as in panel A: PP (gp42), gray; HTCP (gp49), blue; HTJP (gp50), green; TrP (gp52), pink; MTP (gp53), yellow. (F) Cutaway view of segmented reconstruction, showing density inside neck, colored as in panel C. In addition, the DNA is purple; TCP (gp51), orange; TMP (gp56), brown.CC BY · PubMed Central
Figure 2. Atomic modeling of the neck. (A) Ribbon representation of the atomic model from the C6 neck reconstruction. The two copies of HTCP (gp49) per asymmetric unit are colored light and dark blue; the HTJP (gp50), TrP (gp52) and MTP (gp53) hexamers are shown in green, pink and yellow, respectively. The C-terminus of HTCP, which was built from the previous portal structure [30] is in cyan. (B) Atomic model of the neck reconstruction with one asymmetric unit colored as in panel A, the rest gray. The previously determined portal protein model is included, with the two copies of PP (gp42) per asymmetric unit colored light and dark brown. (C) An isolated asymmetric unit, colored as in A and B. (D) Slab through the neck model, colored as in panel A. (E) Sections through the neck model at the levels indicated by the arrows in panel D. From left to right: HTCP and HTJP; HTJP and TrP; TrP and MTP. The smallest inner diameters are indicated. (F) Monomers of neck proteins, from left to right: HTCP, HTJP, TrP and MTP. (G) Interaction between HTJP (green surface) and the HTCP (blue) and TrP (pink). (H) Interaction between HTJP (green), HTCP (blue) and TrP (pink) shown as molecular surfaces. (I) Cutaway view showing the electrostatic potential surface of the tail interior. (J) AlphaFold model of HTJP (orange) superimposed on the HTJP model from the neck reconstruction (green), showing the predicted inner ring of α-helices. (K) MTPs from the 80α baseplate reconstruction (orange and tan) superimposed on the MTP from the neck model (yellow), showing the difference in the C-arm.
Figure 2. Atomic modeling of the neck. (A) Ribbon representation of the atomic model from the C6 neck reconstruction. The two copies of HTCP (gp49) per asymmetric unit are colored light and dark blue; the HTJP (gp50), TrP (gp52) and MTP (gp53) hexamers are shown in green, pink and yellow, respectively. The C-terminus of HTCP, which was built from the previous portal structure [30] is in cyan. (B) Atomic model of the neck reconstruction with one asymmetric unit colored as in panel A, the rest gray. The previously determined portal protein model is included, with the two copies of PP (gp42) per asymmetric unit colored light and dark brown. (C) An isolated asymmetric unit, colored as in A and B. (D) Slab through the neck model, colored as in panel A. (E) Sections through the neck model at the levels indicated by the arrows in panel D. From left to right: HTCP and HTJP; HTJP and TrP; TrP and MTP. The smallest inner diameters are indicated. (F) Monomers of neck proteins, from left to right: HTCP, HTJP, TrP and MTP. (G) Interaction between HTJP (green surface) and the HTCP (blue) and TrP (pink). (H) Interaction between HTJP (green), HTCP (blue) and TrP (pink) shown as molecular surfaces. (I) Cutaway view showing the electrostatic potential surface of the tail interior. (J) AlphaFold model of HTJP (orange) superimposed on the HTJP model from the neck reconstruction (green), showing the predicted inner ring of α-helices. (K) MTPs from the 80α baseplate reconstruction (orange and tan) superimposed on the MTP from the neck model (yellow), showing the difference in the C-arm.CC BY · PubMed Central
Figure 3. Modeling of the inside of the neck. (A) Detail of internal density with the TCP (gp50, orange), TMP (gp56, shades of green) and DNA (purple) models fitted in. External proteins (HTCP, HTJP, TrP and MTP) are colored as in Fig. 2. (B) Atomic model of the inside of the neck, including the DNA double helix (purple and magenta), TCP (orange) and the three copies of TMP in green, turquoise and aqua, inside the segmented density of the asymmetric reconstruction. (C) Same model as in (B) with the atomic model of the surrounding proteins shown in gray. (D) slabs through the tail model at the levels indicated in (C). (E) Closeup view of the internal proteins and the DNA. (F) Ribbon diagram of the TCP model. (G) Ribbon diagrams of the AlphaFold3 models of the TCPs from phage lambda (gpZ), HK97 (gp10) and SPP1 (gp16.1). (H) The interaction between TCP, TMP and the DNA. The TCP interacting loop is shown in stick representation, colored by element. (I) Detail of the interaction between TCP and the DNA. The 3’ and 5’ ends of the DNA and pertinent residues are indicated. (J) Electrostatic potential surfaces of the inside of the tail. (K) Electrostatic surface of TCP with surrounding proteins and DNA shown in ribbon representation. (L) Top view of the electrostatic surface of TCP with the HTCP shown in ribbon representation. (K) Same view as panel L with TCP and HTCP both shown as electrostatic surfaces.
Figure 3. Modeling of the inside of the neck. (A) Detail of internal density with the TCP (gp50, orange), TMP (gp56, shades of green) and DNA (purple) models fitted in. External proteins (HTCP, HTJP, TrP and MTP) are colored as in Fig. 2. (B) Atomic model of the inside of the neck, including the DNA double helix (purple and magenta), TCP (orange) and the three copies of TMP in green, turquoise and aqua, inside the segmented density of the asymmetric reconstruction. (C) Same model as in (B) with the atomic model of the surrounding proteins shown in gray. (D) slabs through the tail model at the levels indicated in (C). (E) Closeup view of the internal proteins and the DNA. (F) Ribbon diagram of the TCP model. (G) Ribbon diagrams of the AlphaFold3 models of the TCPs from phage lambda (gpZ), HK97 (gp10) and SPP1 (gp16.1). (H) The interaction between TCP, TMP and the DNA. The TCP interacting loop is shown in stick representation, colored by element. (I) Detail of the interaction between TCP and the DNA. The 3’ and 5’ ends of the DNA and pertinent residues are indicated. (J) Electrostatic potential surfaces of the inside of the tail. (K) Electrostatic surface of TCP with surrounding proteins and DNA shown in ribbon representation. (L) Top view of the electrostatic surface of TCP with the HTCP shown in ribbon representation. (K) Same view as panel L with TCP and HTCP both shown as electrostatic surfaces.CC BY · PubMed Central

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Metadata

Authors
Kizziah, J. L., Mukherjee, A., Parker, L. K., & Dokland, T.
Affiliations
University of Alabama at Birmingham (US)
Corresponding author
Dokland, Terje
ORCID
Venue
Structure
Publisher
Elsevier BV
Published
2025-06
Volume
33
Issue
6
Pages
1063-1073.e2
ISSN
0969-2126 (ISSN-L)
DOI
10.1016/j.str.2025.03.007
PMC
PMC11661146
OpenAlex
W4409139676
Cited by
11
References
65
Citations by year
2026: 9 · 2025: 2
FWCI
2.71
Type
journal article
Language
en
Open access
Licence
Locations
  • Structure (acceptedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed Central (submittedVersion, cc-by)
Funders
  • National Institute of General Medical Sciences (U24 GM116789)
  • University of Alabama at Birmingham (SCR_025450)
  • Purdue University (U24 GM116789)
  • National Institutes of Health Office of the Director
  • National Institute of Allergy and Infectious Diseases Division of Microbiology and Infectious Diseases (R01 AI083255)
  • National Institutes of Health (SCR_025545)
Topics
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
  • Health Sciences › Medicine › Infectious Diseases › Antimicrobial Resistance in Staphylococcus
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
pathogenicity islands, mobile genetic elements, portal vertex, tape measure protein, viral assembly

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