Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy

Kamiya, Ryosuke; Uchiyama, Jumpei; Matsuzaki, Shigenobu; Murata, Kazuyoshi; Iwasaki, Katsunori; Miyazaki, Naoyuki

doi:10.1016/j.str.2021.09.001

Cited by 9 publications

(6 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These involve a large cluster of charged residues, including E201, K210, K247, D249, E251, D260, and R264, which form complimentary interactions. Finally, compared to other known phage capsid structures (Kamiya et al, 2021; Wikoff et al, 2000), the MCP of ϕKp24 displayed a structural feature that has, to our knowledge, not been previously reported: the long C-terminal loop (residues Q582-S597) participates in the formation of a pore with an inner diameter of approximately 2 nm (Figure. 1E, right upper and lower panels).…”

Section: Resultsmentioning

confidence: 72%

High resolution reconstruction of a Jumbo bacteriophage infecting capsulated bacteria using hyperbranched tail fibers

Ouyang

Costa

Cassidy

et al. 2022

Preprint

View full text Add to dashboard Cite

The Klebsiella jumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combined cryo-electron microscopy methods, protein structure prediction methods, molecular simulations, and machine learning approaches to explore the capsid, tail, and tail fibers of this phage at high resolution. We determined the structure of the capsid and tail at 4.3 Angstrom and 4.1 Angstrom resolution. We observed that the tail fibers were highly branched and rearranged dramatically upon cell surface attachment. This complex configuration involves fourteen putative tail fibers with depolymerase activity that provide ϕKp24 with the ability to infect a broad panel of capsular polysaccharide (CPS) types of Klebsiella pneumoniae. Taken together, our study provides structural and functional insight into how ϕKp24 adapts to the highly variable surfaces of capsulated bacterial pathogens, which will be useful for the development of phage therapy approaches against pan-drug resistant K. pneumoniae strains.

show abstract

Section: Resultsmentioning

confidence: 72%

High resolution reconstruction of a Jumbo bacteriophage infecting capsulated bacteria using hyperbranched tail fibers

Ouyang

Costa

Cassidy

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…The overall conformations of the central and surrounding hexamers are quite similar, displaying a backbone root-mean-square displacement (RMSD) of ~1.5 Å. Finally, compared to other known phage capsid structures 23 , 24 , the MCP of ϕKp24 displayed a structural feature that has, to our knowledge, not been previously reported: each of the six long C-terminal loops (residues Q582-S597) participate in the formation of a central helical pore with an outer diameter of ~2 nm (Fig. 1e , right upper and lower panels).…”

Section: Resultsmentioning

confidence: 96%

High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers

et al. 2022

View full text Add to dashboard Cite

The Klebsiella jumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combine cryo-electron microscopy methods, protein structure prediction methods, molecular simulations, microbiological and machine learning approaches to explore the capsid, tail, and tail fibers of ϕKp24. We determine the structure of the capsid and tail at 4.1 Å and 3.0 Å resolution. We observe the tail fibers are branched and rearranged dramatically upon cell surface attachment. This complex configuration involves fourteen putative tail fibers with depolymerase activity that provide ϕKp24 with the ability to infect a broad panel of capsular polysaccharide (CPS) types of Klebsiella pneumoniae. Our study provides structural and functional insight into how ϕKp24 adapts to the variable surfaces of capsulated bacterial pathogens, which is useful for the development of phage therapy approaches against pan-drug resistant K. pneumoniae strains.

show abstract

“…This capsid geometry was previously reported in Shigella myophages (Doore et al, 2018 ), in coliphage N4 ( Podoviridae ) (Choi et al, 2008 ), Bacillus phage Basilisk (Grose et al, 2014 ) and Mycobacterium phage Rosebush (Podgorski et al, 2020 ) (both members of the Siphoviridae family). This larger triangulation number facilitates the packing of a larger genome of ~98 kb (Doore et al, 2018 ; Kamiya et al, 2021 ). At the interior of the capsid the arrangement of the dsDNA genome is visible as a series of layers separated by ~23 Å [Figure 2(D) ].…”

Section: Resultsmentioning

confidence: 99%

A lipopolysaccharide‐dependent phage infects a pseudomonad phytopathogen and can evolve to evade phage resistance

Warring

Malone

Jayaraman

et al. 2022

Environmental Microbiology

View full text Add to dashboard Cite

Bacterial pathogens are major causes of crop diseases, leading to significant production losses. For instance, kiwifruit canker, caused by the phytopathogen Pseudomonas syringae pv. actinidiae (Psa), has posed a global challenge to kiwifruit production. Treatment with copper and antibiotics, whilst initially effective, is leading to the rise of bacterial resistance, requiring new biocontrol approaches. Previously, we isolated a group of closely related Psa phages with biocontrol potential, which represent environmentally sustainable antimicrobials. However, their deployment as antimicrobials requires further insight into their properties and infection strategy. Here, we provide an in‐depth examination of the genome of ΦPsa374‐like phages and show that they use lipopolysaccharides (LPS) as their main receptor. Through proteomics and cryo‐electron microscopy of ΦPsa374, we revealed the structural proteome and that this phage possess a T = 9 capsid triangulation, unusual for myoviruses. Furthermore, we show that ΦPsa374 phage resistance arises in planta through mutations in a glycosyltransferase involved in LPS synthesis. Lastly, through in vitro evolution experiments we showed that phage resistance is overcome by mutations in a tail fibre and structural protein of unknown function in ΦPsa374. This study provides new insight into the properties of ΦPsa374‐like phages that informs their use as antimicrobials against Psa.

show abstract

Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy

Abstract: Highlights d Cryo-EM capsid structures of Helicobacter pylori phages KHP30 and KHP40 d Phage capsid structures in T = 9 icosahedral symmetry d Structural insights into particle stability in acid conditions d Possible mechanism of phage adaptation to the human gastric environment

Cited by 9 publications

References 59 publications

High resolution reconstruction of a Jumbo bacteriophage infecting capsulated bacteria using hyperbranched tail fibers

High resolution reconstruction of a Jumbo bacteriophage infecting capsulated bacteria using hyperbranched tail fibers

High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers

A lipopolysaccharide‐dependent phage infects a pseudomonad phytopathogen and can evolve to evade phage resistance

Contact Info

Product

Resources

About