Competing scaffolding proteins determine capsid size during mobilization of Staphylococcus aureus pathogenicity islands

Dearborn, Altaira D.; Wall, Erin A.; Kizziah, James L.; Klenow, Laura; Parker, Laura; Manning, Keith A.; Spilman, Michael; Spear, John; Christie, Gail E.; Dokland, Terje

doi:10.7554/elife.30822

Cited by 52 publications

(71 citation statements)

References 45 publications

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“…Cryo-EM samples were prepared on nickel Quantifoil R2/1 grids, as previously described [15]. An initial cryo-EM data set consisting of 51 images was collected on SO-163 film on a Philips CM20 FEG microscope.…”

Section: Electron Microscopymentioning

confidence: 99%

“…Phage 80α is a typical staphylococcal siphovirus with a 43.8 kbp genome and a 63 nm icosahedral capsid, attached to a 190 nm long flexuous tail that is capped by an ornate baseplate [14][15][16]. 80α is one of the best-described S. aureus phages, and is closely related to ϕETA2 and other phages involved in specifying bacterial pathogenicity [14].…”

Section: Introductionmentioning

confidence: 99%

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Structure of the host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage

et al. 2020

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Staphylococcus aureus is a common cause of infections in humans. The emergence of virulent, antibiotic-resistant strains of S. aureus is a significant public health concern. Most virulence and resistance factors in S. aureus are encoded by mobile genetic elements, and transduction by bacteriophages represents the main mechanism for horizontal gene transfer. The baseplate is a specialized structure at the tip of bacteriophage tails that plays key roles in host recognition, cell wall penetration, and DNA ejection. We have used high-resolution cryo-electron microscopy to determine the structure of the S. aureus bacteriophage 80α baseplate at 3.75 Å resolution, allowing atomic models to be built for most of the major tail and baseplate proteins, including two tail fibers, the receptor binding protein, and part of the tape measure protein. Our structure provides a structural basis for understanding host recognition, cell wall penetration and DNA ejection in viruses infecting Gram-positive bacteria. Comparison to other phages demonstrates the modular design of baseplate proteins, and the adaptations to the host that take place during the evolution of staphylococci and other pathogens. Author summaryThe emergence of virulent strains of Staphylococcus aureus that are resistant to most antibiotics has become a major public health concern. Virulence and resistance determinants in S. aureus are usually carried on mobile genetic elements (MGEs). Transduction by bacteriophages provides the main means by which MGEs are disseminated horizontally through the bacterial population, and is therefore essential to the evolution of pathogenicity of S. aureus and other pathogens. The baseplate is a complex structure at the tip of bacteriophage tails that serves multiple roles, including host recognition and binding, cell wall penetration, and ejection of the phage DNA. We have determined the structure of the baseplate from bacteriophage 80α, a representative of phages involved in host pathogenicity and in the mobilization of MGEs in S. aureus. Our structure provides a basis for understanding host recognition and infection by phages infecting Gram-positive hosts, and the PLOS Pathogens | https://doi.

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Section: Electron Microscopymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Structure of the host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage

et al. 2020

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“…The E-loop has been implicated in making contacts with the P-domain and A-domain of the adjacent subunits in phages such as phi29 (20),T4 (10, 23), T7 (22), HSV-1 (21) and 80 alpha (45). It also makes intercapsomer contacts in the capsid of the HK97 phage that are important for procapsid assembly and are only found in procapsids (29).…”

Section: Discussionmentioning

confidence: 99%

A hydrophobic network: Intersubunit and intercapsomer interactions stabilizing the bacteriophage P22 capsid

Asija

Teschke

2019

Preprint

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19dsDNA tailed phages and herpesviruses assemble their capsids using coat proteins that 20 have the ubiquitous HK97 fold. Though this fold is common, we do not have a thorough 21 understanding of the different ways viruses adapt it to maintain stability in various environments. 22The HK97-fold E-loop, which connects adjacent subunits at the outer periphery of capsomers, 23 has been implicated in capsid stability. Here we show that in bacteriophage P22, residue W61 24 at the tip of the E-loop plays a role in stabilizing procapsids and in maturation. We hypothesize 25 that a hydrophobic pocket is formed by residues I366 and W410 in the P-domain of a 26 neighboring subunit within a capsomer, into which W61 fits like a peg. In addition, W61 likely 27 bridges to residues A91 and L401 in P-domain loops of an adjacent capsomer, thereby linking 28 the entire capsid together with a network of hydrophobic interactions. There is conservation of 29 this hydrophobic network in the distantly related P22-like phages, indicating that this structural 30 feature is likely important for stabilizing this family of phages. Thus, our data shed light on one 31 of the varied elegant mechanisms used in nature to consistently build stable viral genome 32 containers through subtle adaptation of the HK97 fold.33 34 IMPORTANCE 35Similarities in assembly reactions and coat protein structures of the dsDNA tailed 36 phages and herpesviruses make phages ideal models to understand capsid assembly and 37 identify potential targets for antiviral drug discovery. The coat protein E-loops of these viruses 38 are involved in both intra-and intercapsomer interactions. In phage P22, hydrophobic 39 interactions peg the coat protein subunits together within a capsomer, where the E-loop 40 hydrophobic residue W61 of one subunit packs into a pocket of hydrophobic residues I366 and 41 W410 of the adjacent subunit. W61 also makes hydrophobic interactions with A91 and L401 of a 42 subunit in an adjacent capsomer. We show these intra-and intercapsomer hydrophobic 43 interactions form a network crucial to capsid stability and proper assembly. 48protein assembly catalyst, scaffolding protein (1). Following the formation of the DNA-free 49 precursor capsid (procapsid), the DNA is packaged through the portal ring resulting in increases 50 in the capsid volume and stability. This step is generally termed capsid expansion or maturation 51 (2). The addition of the tail machinery marks the end of assembly (2). The three-dimensional 52 arrangement of coat proteins in dsDNA viral capsids results in robust structures that can 53 withstand high levels of internal pressure that is exerted by packaged DNA, which results in 54 repulsive forces as well as the energetic strain imposed from DNA bending (3)(4)(5). In phages 55 such as phi29 the pressure inside a capsid is known to exceed 6 MPa (6). In some phages, this 56 pressure is thought to be necessary to eject the DNA into the prokaryotic host. 57The presence of a common Hong Kong 97 fold (HK97 fold) in the coat proteins of ...

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“…Patience also has a decoration protein that links the minor coat proteins together and makes no contact with the major capsid protein ( Figure 5). The major capsid proteins that make up the hexamers (Figure 4) have an arrangement that appears similar to the 80alpha bacteriophage procapsid (EMD-7030) [31]. The internal diameter of the capsid is 63.5 nm.…”

Section: Capsid Morphologies and Accessory Proteinsmentioning

confidence: 98%

Structures of three actinobacteriophage capsids: Roles of symmetry and accessory proteins

Calabrese

Alexandrescu

et al. 2020

Preprint

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Mycobacterium tuberculosis and abscessus are major human pathogens that are part of the Actinobacteria phylum. Increasing multiple drug resistance in these bacteria has led to a renewed interest in using viruses that infect these bacteria for therapy. In order to understand these viruses, a course-based undergraduate research experience (CURE) program run by SEA-PHAGES at the University of Pittsburgh and HHMI has isolated, sequenced, and annotated over 3000 actinobacteriophages (viruses that infect Actinobacteria). Little work has been done to investigate the structural diversity of these phage, all of which are thought to use a common protein fold, the HK97-fold, in their major capsid protein. Here we describe the structure of three actinobacteriophage capsids isolated by students that infect Mycobacterium smegmatis. The capsid structures were resolved to approximately 6 angstroms, which allowed confirmation that each phage uses the HK97-fold to form their capsid. One phage, Rosebush, has a novel variation of the HK97-fold. Four novel accessory proteins, that form the capsid head along with the major capsid protein, were identified that show limited or no homology to known proteins. The genes that encode the proteins were identified using SDS-PAGE and mass spectrometry. Bioinformatic analysis of the accessory proteins suggest they are used in many actinobacteriophage capsids.

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Competing scaffolding proteins determine capsid size during mobilization of Staphylococcus aureus pathogenicity islands

Cited by 52 publications

References 45 publications

Structure of the host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage

Structure of the host cell recognition and penetration machinery of a Staphylococcus aureus bacteriophage

A hydrophobic network: Intersubunit and intercapsomer interactions stabilizing the bacteriophage P22 capsid

Structures of three actinobacteriophage capsids: Roles of symmetry and accessory proteins

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