Structure of Escherichia coli O157:H7 bacteriophage CBA120 tailspike protein 4 baseplate anchor and tailspike assembly domains (TSP4-N)

Chao, Kinlin; Shang, Xiaoran; Greenfield, Julia; Linden, Sara B.; Alreja, Adit B.; Nelson, Daniel; Herzberg, Osnat

doi:10.1038/s41598-022-06073-2

Cited by 12 publications

(27 citation statements)

References 33 publications

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“…To confirm that SPTD1 utilized a branched RBP complex, which is typical of Ackermannviridae family members, the genomic sequence of SPTD1 was examined, annotated, and submitted to GenBank (OP991882). Whole genome BLAST ® analysis of SPTD1 revealed significant DNA homology (97% identity over 91% coverage) to CBA120 (JN593240), a prototypical member of the Ackermannviridae family with a well-described TSP complex [ 27 , 28 , 38 , 39 , 40 , 47 ]. Upon inspection, SPTD1 was found to possess homologs of each CBA120 TSP ( Figure 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…Substantial N-terminal amino acid sequence similarity between CBA120 and SPTD1 TSPs, ranging from 59% identity for TSP1 to over 96% identity for TSP2, TSP3, and TSP4 was observed. The N-terminus of these TSPs serves an essential structural role, mediating both attachment to the baseplate (TSP4) and facilitating complex assembly through TSP interactions (TSP1-4) [ 27 , 40 ]. In contrast to the N-terminus, less than 20% amino acid identity was observed in the remaining sections of each protein.…”

Section: Resultsmentioning

confidence: 99%

“…Sequence comparisons between the TSP clusters of CBA120 and SPTD1 were performed using EMBOSS Needle with default settings [ 36 , 37 ]. For sequence comparison, delineation of N- and C-terminal domains was based upon known crystal structures of CBA120’s TSP1-4 [ 27 , 38 , 39 , 40 ]. Whole genome comparisons and all other amino acid analyses were performed using BLAST ® with default settings [ 41 ].…”

Section: Methodsmentioning

confidence: 99%

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Tailoring the Host Range of Ackermannviridae Bacteriophages through Chimeric Tailspike Proteins

Gil

Paulson

Brown

et al. 2023

Viruses

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Host range is a major determinant in the industrial utility of a bacteriophage. A model host range permits broad recognition across serovars of a target bacterium while avoiding cross-reactivity with commensal microbiota. Searching for a naturally occurring bacteriophage with ideal host ranges is challenging, time-consuming, and restrictive. To address this, SPTD1.NL, a previously published luciferase reporter bacteriophage for Salmonella, was used to investigate manipulation of host range through receptor-binding protein engineering. Similar to related members of the Ackermannviridae bacteriophage family, SPTD1.NL possessed a receptor-binding protein gene cluster encoding four tailspike proteins, TSP1-4. Investigation of the native gene cluster through chimeric proteins identified TSP3 as the tailspike protein responsible for Salmonella detection. Further analysis of chimeric phages revealed that TSP2 contributed off-target Citrobacter recognition, whereas TSP1 and TSP4 were not essential for activity against any known host. To improve the host range of SPTD1.NL, TSP1 and TSP2 were sequentially replaced with chimeric receptor-binding proteins targeting Salmonella. This engineered construct, called RBP-SPTD1-3, was a superior diagnostic reporter, sensitively detecting additional Salmonella serovars while also demonstrating improved specificity. For industrial applications, bacteriophages of the Ackermannviridae family are thus uniquely versatile and may be engineered with multiple chimeric receptor-binding proteins to achieve a custom-tailored host range.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Tailoring the Host Range of Ackermannviridae Bacteriophages through Chimeric Tailspike Proteins

Gil

Paulson

Brown

et al. 2023

Viruses

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“…In contrast, KP1.peg.142 matched poorly with 102 l (TM-align score: 0.2787) yet showed a high similarity with the phage T4 cell–puncturing device (PDB ID: 1 K28) with a TM-align score of 0.98305. Furthermore, homotrimer structure prediction of KP1.peg.142 identified a triple β-helix domain—a structure often found in the C-terminus of phage T4 baseplate protein Gp5 ( Kanamaru et al, 2002 ; Weigele et al, 2003 ; Chao et al, 2022 ; Supplementary Figure S6A ). Therefore, it is likely that KP1.peg.110 encodes for an endolysin whereas KP1.peg.142 encodes for a tail lysozyme ( Supplementary Table S2 ).…”

Section: Resultsmentioning

confidence: 99%

Characterization of Klebsiella pneumoniae bacteriophages, KP1 and KP12, with deep learning-based structure prediction

et al. 2023

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Concerns over Klebsiella pneumoniae resistance to the last-line antibiotic treatment have prompted a reconsideration of bacteriophage therapy in public health. Biotechnological application of phages and their gene products as an alternative to antibiotics necessitates the understanding of their genomic context. This study sequenced, annotated, characterized, and compared two Klebsiella phages, KP1 and KP12. Physiological validations identified KP1 and KP12 as members of Myoviridae family. Both phages showed that their activities were stable in a wide range of pH and temperature. They exhibit a host specificity toward K. pneumoniae with a broad intraspecies host range. General features of genome size, coding density, percentage GC content, and phylogenetic analyses revealed that these bacteriophages are distantly related. Phage lytic proteins (endolysin, anti-/holin, spanin) identified by the local alignment against different databases, were subjected to further bioinformatic analyses including three-dimensional (3D) structure prediction by AlphaFold. AlphaFold models of phage lysis proteins were consistent with the published X-ray crystal structures, suggesting the presence of T4-like and P1/P2-like bacteriophage lysis proteins in KP1 and KP12, respectively. By providing the primary sequence information, this study contributes novel bacteriophages for research and development pipelines of phage therapy that ultimately, cater to the unmet clinical and industrial needs against K. pneumoniae pathogens.

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“…Most phages have polyhedral capsids, predominantly icosahedral, except for filamentous ones [ 35 ]. The structure of tailed phages consists of an icosahedral head and a tail with receptor-binding proteins (RBPs) such as tail spikes and tail fibers at the distal end [ 36 , 37 ]. Phage genomes containing single-stranded or double-stranded RNA or DNA are encased in the protein capsid.…”

Section: Phage Structure and Life Cyclementioning

confidence: 99%

Evolutionary Dynamics between Phages and Bacteria as a Possible Approach for Designing Effective Phage Therapies against Antibiotic-Resistant Bacteria

Hasan

Ahn

2022

Antibiotics

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With the increasing global threat of antibiotic resistance, there is an urgent need to develop new effective therapies to tackle antibiotic-resistant bacterial infections. Bacteriophage therapy is considered as a possible alternative over antibiotics to treat antibiotic-resistant bacteria. However, bacteria can evolve resistance towards bacteriophages through antiphage defense mechanisms, which is a major limitation of phage therapy. The antiphage mechanisms target the phage life cycle, including adsorption, the injection of DNA, synthesis, the assembly of phage particles, and the release of progeny virions. The non-specific bacterial defense mechanisms include adsorption inhibition, superinfection exclusion, restriction-modification, and abortive infection systems. The antiphage defense mechanism includes a clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) system. At the same time, phages can execute a counterstrategy against antiphage defense mechanisms. However, the antibiotic susceptibility and antibiotic resistance in bacteriophage-resistant bacteria still remain unclear in terms of evolutionary trade-offs and trade-ups between phages and bacteria. Since phage resistance has been a major barrier in phage therapy, the trade-offs can be a possible approach to design effective bacteriophage-mediated intervention strategies. Specifically, the trade-offs between phage resistance and antibiotic resistance can be used as therapeutic models for promoting antibiotic susceptibility and reducing virulence traits, known as bacteriophage steering or evolutionary medicine. Therefore, this review highlights the synergistic application of bacteriophages and antibiotics in association with the pleiotropic trade-offs of bacteriophage resistance.

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Structure of Escherichia coli O157:H7 bacteriophage CBA120 tailspike protein 4 baseplate anchor and tailspike assembly domains (TSP4-N)

Cited by 12 publications

References 33 publications

Tailoring the Host Range of Ackermannviridae Bacteriophages through Chimeric Tailspike Proteins

Tailoring the Host Range of Ackermannviridae Bacteriophages through Chimeric Tailspike Proteins

Characterization of Klebsiella pneumoniae bacteriophages, KP1 and KP12, with deep learning-based structure prediction

Evolutionary Dynamics between Phages and Bacteria as a Possible Approach for Designing Effective Phage Therapies against Antibiotic-Resistant Bacteria

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