Cryo-EM Structure of a Kinetically Trapped Dodecameric Portal Protein from the Pseudomonas-phage PaP3

Hou, Chun-Feng David; Swanson, Nicholas; Li, Fenglin; Yang, Ruoyu; Lokareddy, Ravi K.; Cingolani, Gino

doi:10.1016/j.jmb.2022.167537

Cited by 7 publications

(4 citation statements)

References 86 publications

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“…Tridecamers, like those we observed here, were also found for Bacillus phage SPP1 [40,47,48]; Salmonella phage P22 formed undecamers and dodecamers [48], while a distribution from 11-to 14-mer was observed for herpes simplex virus 1 [49]. Asymmetric oligomers are also observed, including spiraling forms or rings appearing to be missing one or more subunits [50,51].…”

Section: Discussionsupporting

confidence: 80%

Structure of the portal complex fromStaphylococcus aureuspathogenicity island 1 transducing particles in situ and in solution

Mukherjee,

Kizziah,

Hawkins

et al. 2023

Preprint

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Staphylococcus aureusis an important human pathogen, and the prevalence of antibiotic resistance is a major public health concern. The evolution of pathogenicity and resistance inS. aureusoften involves acquisition of mobile genetic elements (MGEs). Bacteriophages play an especially important role, since transduction represents the main mechanism for horizontal gene transfer.S. aureuspathogenicity islands (SaPIs), including SaPI1, are MGEs that carry genes encoding virulence factors, and are mobilized at high frequency through interactions with specific helper bacteriophages, such as 80α, leading to packaging of the SaPI genomes into virions made from structural proteins supplied by the helper. Among these structural proteins is the portal protein, which forms a ring-like portal at a fivefold vertex of the capsid, through which the DNA is packaged during virion assembly and ejected upon infection of the host. We have used high-resolution cryo-electron microscopy to determine structures of theS. aureusbacteriophage 80α portal in solution and in situ in the empty and full SaPI1 virions, and show how the portal interacts with the capsid. These structures provide a structural basis for understanding portal and capsid assembly and the conformational changes that occur upon DNA packaging and ejection.

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Section: Discussionsupporting

confidence: 80%

Structure of the portal complex fromStaphylococcus aureuspathogenicity island 1 transducing particles in situ and in solution

Mukherjee,

Kizziah,

Hawkins

et al. 2023

Preprint

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show abstract

“…S4). The wing, clip, and stem are structurally continuous and form the portal body, whereas the crown and barrel do not make intramolecular contact with the rest of the protomer tertiary structure and are highly dynamic, possibly moving like a lever ( 40 ). A Dali ( 41 ) search identified the related phage P22 portal protein ( 42 – 44 ) as the most similar to the Sf6 portal protomer described here (table S1).…”

Section: Resultsmentioning

confidence: 99%

“…S5B). This modest binding interface suggests that isolated barrel helices do not form a stable quaternary structure in solution ( 40 ) or procapsid ( 44 ) but assemble into a tunnel when stabilized by surrounding DNA and possibly ejection proteins ( 36 ). As reported for other phages, a ring of electron density around the portal perimeter ( 44 , 46 ) corresponding to double-stranded DNA (dsDNA) ( Fig.…”

Section: Resultsmentioning

confidence: 99%

High-resolution cryo-EM structure of the Shigella virus Sf6 genome delivery tail machine

Hou

Yang

et al. 2022

Sci. Adv.

Self Cite

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Sf6 is a bacterial virus that infects the human pathogen Shigella flexneri. Here, we describe the cryo–electron microscopy structure of the Sf6 tail machine before DNA ejection, which we determined at a 2.7-angstrom resolution. We built de novo structures of all tail components and resolved four symmetry-mismatched interfaces. Unexpectedly, we found that the tail exists in two conformations, rotated by ~6° with respect to the capsid. The two tail conformers are identical in structure but differ solely in how the portal and head-to-tail adaptor carboxyl termini bond with the capsid at the fivefold vertex, similar to a diamond held over a five-pronged ring in two nonidentical states. Thus, in the mature Sf6 tail, the portal structure does not morph locally to accommodate the symmetry mismatch but exists in two energetic minima rotated by a discrete angle. We propose that the design principles of the Sf6 tail are conserved across P22-like Podoviridae.

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“…Portal proteins are dodecameric assemblies, mainly found in tailed bacteriophages and herpesvirus [ 70 ]. The portal protein functions as a bidirectional gateway through which a virus can exchange DNA with the outside environment [ 71 ]. During virus morphogenesis, the portal protein recruits small and large terminase subunits that assemble to form a genome-packaging motor [ 72 ].…”

Section: Discussionmentioning

confidence: 99%

Bacterial isolation and genome analysis of a novel Klebsiella quasipneumoniae phage in southwest China’s karst area

Liu,

Wang,

Zhao

et al. 2024

Virol J

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Background Southwest China is one of the largest karst regions in the world. Karst environment is relatively fragile and vulnerable to human activities. Due to the discharge of sewage and domestic garbage, the karst system may be polluted by pathogenic bacteria. The detection of bacterial distribution and identification of phage capable of infecting them is an important approach for environmental assessment and resource acquisition. Methods Bacteria and phages were isolated from karst water in southwest China using the plate scribing and double plate method, respectively. Isolated phage was defined by transmission electron microscopy, one-step growth curve and optimal multiplicity of infection (MOI). Genomic sequencing, phylogenetic analysis, comparative genomic and proteomic analysis were performed. Results A Klebsiella quasipneumoniae phage was isolated from 32 isolates and named KL01. KL01 is morphologically identified as Caudoviricetes with an optimal MOI of 0.1, an incubation period of 10 min, and a lysis period of 60 min. The genome length of KL01 is about 45 kb, the GC content is 42.5%, and it contains 59 open reading frames. The highest average nucleotide similarity between KL01 and a known Klebsiella phage 6939 was 83.04%. Conclusions KL01 is a novel phage, belonging to the Autophagoviridae, which has strong lytic ability. This study indicates that there were not only some potential potentially pathogenic bacteria in the karst environment, but also phage resources for exploration and application.

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Cryo-EM Structure of a Kinetically Trapped Dodecameric Portal Protein from the Pseudomonas-phage PaP3

Cited by 7 publications

References 86 publications

Structure of the portal complex fromStaphylococcus aureuspathogenicity island 1 transducing particles in situ and in solution

Structure of the portal complex fromStaphylococcus aureuspathogenicity island 1 transducing particles in situ and in solution

High-resolution cryo-EM structure of the Shigella virus Sf6 genome delivery tail machine

Bacterial isolation and genome analysis of a novel Klebsiella quasipneumoniae phage in southwest China’s karst area

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