Structure and host specificity of
            <i>Staphylococcus epidermidis</i>
            bacteriophage Andhra

Hawkins, N’Toia C.; Kizziah, James L.; Hatoum-Aslan, Asma; Dokland, Terje

doi:10.1126/sciadv.ade0459

Cited by 13 publications

(12 citation statements)

References 75 publications

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“…The entire structure is shown in the inset. (D) Superposition of the 80a in situ PP (blue) with the PP from phage Andhra (orange; PDB ID: 8EGR) [42].…”

Section: Resultsmentioning

confidence: 99%

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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“…The entire structure is shown in the inset. (D) Superposition of the 80a in situ PP (blue) with the PP from phage Andhra (orange; PDB ID: 8EGR) [42].…”

Section: Resultsmentioning

confidence: 99%

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

Mukherjee,

Kizziah,

Hawkins

et al. 2023

Preprint

Self Cite

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“…This small podophage is a typical member of the Andhravirus genus (Rountreeviridae family). Like its close relatives, namely Staphylococcus phages Andhra [46,48], BESEP3 (GenBank: MT596500.1), and SeAlphi (NCBI: NC_070880.1), the bacterial host of St_134 is S. epidermidis. Several other coagulase-negative Staphylococcus species were sensitive to St_134, including S. haemolyticus.…”

Section: Discussionmentioning

confidence: 99%

“…The cysteine, histidine-dependent amidohydrolases/peptidases (CHAP) hydrolyze peptidoglycans in the bacterial cell wall. AlphaFold2 showed that the putative 3D structure of LysSte134_2 is similar to the Andhra gp10 protein [46]. In LysSte134_2, the N-terminal globular core contains the predicted enzymatic GyH-like domain and connects to the C-terminal globular CHAP domain via an ordered linker domain (middle linker).…”

Section: In Silico Characterization Of St_134 Lysinsmentioning

confidence: 99%

Bacteriophage St_134 and its Endolysin as a Potential Staphy-lococcus Biofilm-Removing Biological Agent

Golosova,

Matveev,

Tikunova

et al. 2023

Preprint

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Bacteria of the genus Staphylococcus are a significant a challenge for medicine, as many species are resistant to multiple antibiotics and even to all of the antibiotics used. One of the approaches to develop new therapeutics to treat staphylococcal infections is the use of bacteriophages specif-ic to these bacteria or lysins of such bacteriophages capable to hydrolyze the cell walls of these bacteria. In this study, a new bacteriophage St_134 specific to Staphylococcus epedermidis was de-scribed. This small podophage belonging to the Andhravirus genus showed relatively wide host range and was able to infect more than 60 strain of Staphylococcus spp., including a clinical strain from the Staphylococcus aureus complex. Two genes encoding different phage lysins were identi-fied in the Ste134 genome. Both lysins LysSte134_1 and LysSte134_2 were produced in Escherichia coli cells. Endolysin LysSte134_1 was demonstrated catalytic activity against a wide panel of staphylococcal peptidoglycans (4 species, 6 strains), was active against S. aureus and S. epidermidis planktonic cultures and destroyed biofilms formed by clinical strains of S. aureus and S. epider-midis.

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“…As well as in the case of eukaryotic viruses mentioned above, AlphaFold predictions can contribute to building the model of the viral particle [ 48 , 103 ] or the virion parts, including the attachment apparatus [ 46 , 50 ] and phage egress machinery [ 51 ]. All the steps of phage infection are accompanied by macromolecular interactions that include proteins, so AlphaFold’s highly accurate structural predictions can assist in the elucidation of the mechanisms of the formation of the phage nucleus [ 49 ], lysogeny maintenance [ 53 ] or anti-phage defence [ 44 , 54 ].…”

Section: Application Of Alphafold For Research On Bacteriophagesmentioning

confidence: 99%

Using AlphaFold Predictions in Viral Research

Gutnik

Evseev

Miroshnikov

et al. 2023

CIMB

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Elucidation of the tertiary structure of proteins is an important task for biological and medical studies. AlphaFold, a modern deep-learning algorithm, enables the prediction of protein structure to a high level of accuracy. It has been applied in numerous studies in various areas of biology and medicine. Viruses are biological entities infecting eukaryotic and procaryotic organisms. They can pose a danger for humans and economically significant animals and plants, but they can also be useful for biological control, suppressing populations of pests and pathogens. AlphaFold can be used for studies of molecular mechanisms of viral infection to facilitate several activities, including drug design. Computational prediction and analysis of the structure of bacteriophage receptor-binding proteins can contribute to more efficient phage therapy. In addition, AlphaFold predictions can be used for the discovery of enzymes of bacteriophage origin that are able to degrade the cell wall of bacterial pathogens. The use of AlphaFold can assist fundamental viral research, including evolutionary studies. The ongoing development and improvement of AlphaFold can ensure that its contribution to the study of viral proteins will be significant in the future.

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Structure and host specificity of Staphylococcus epidermidis bacteriophage Andhra

Cited by 13 publications

References 75 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

Bacteriophage St_134 and its Endolysin as a Potential Staphy-lococcus Biofilm-Removing Biological Agent

Using AlphaFold Predictions in Viral Research

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