Exploitation of a <i>Klebsiella</i> Bacteriophage Receptor-Binding Protein as a Superior Biorecognition Molecule

Nogueira, Catarina; Pires, Diana Priscila Penso; Monteiro, Rodrigo; Santos, Sílvio Roberto Branco; Carvalho, Carla A. O. C. M.

doi:10.1021/acsinfecdis.1c00366

Cited by 20 publications

(12 citation statements)

References 86 publications

(165 reference statements)

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“…We found that the genomes were arranged in a particular disposition: no lysis-specific blocks were distinguished, and structural and morphogenesis-related proteins were repeated in various blocks along the genome (Figure 2). This type of genome, which is not very well organized into functional clusters but shows dispersed agglomerates, has previously been described for big phages of K. pneumoniae, also belonging to the Tevenvirinae subfamily, within which the T4 coliphage is the best studied [19].…”

Section: Genomic Analysis and Comparison Of The Phages Vb_kpnm-vac13 And Vb_kpnm-vac66mentioning

confidence: 59%

Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13

Pacios

Fernández-García

Bleriot

et al. 2021

Viruses

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Klebsiella pneumoniae is a human pathogen that worsens the prognosis of many immunocompromised patients. Here, we annotated and compared the genomes of two lytic phages that infect clinical strains of K. pneumoniae (vB_KpnM-VAC13 and vB_KpnM-VAC66) and phenotypically characterized vB_KpnM-VAC66 (time of adsorption of 12 min, burst size of 31.49 ± 0.61 PFU/infected cell, and a host range of 20.8% of the tested strains). Transmission electronic microscopy showed that vB_KpnM-VAC66 belongs to the Myoviridae family. The genomic analysis of the phage vB_KpnM-VAC66 revealed that its genome encoded 289 proteins. When compared to the genome of vB_KpnM-VAC13, they showed a nucleotide similarity of 97.56%, with a 93% of query cover, and the phylogenetic study performed with other Tevenvirinae phages showed a close common ancestor. However, there were 21 coding sequences which differed. Interestingly, the main differences were that vB_KpnM-VAC66 encoded 10 more homing endonucleases than vB_KpnM-VAC13, and that the nucleotidic and amino-acid sequences of the L-shaped tail fiber protein were highly dissimilar, leading to different three-dimensional protein predictions. Both phages differed significantly in their host range. These viruses may be useful in the development of alternative therapies to antibiotics or as a co-therapy increasing its antimicrobial potential, especially when addressing multidrug resistant (MDR) pathogens.

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Section: Genomic Analysis and Comparison Of The Phages Vb_kpnm-vac13 And Vb_kpnm-vac66mentioning

confidence: 59%

Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13

Pacios

Fernández-García

Bleriot

et al. 2021

Viruses

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“…Thus, the phage tail fiber protein shows a wider host spectrum than the lytic phages because phage infection requires more complex steps. 28 It has been reported that the phage tail spike protein and endolysin have been used as molecular recognition probes for the detection of pathogenic bacteria. 29,30 However, both the proteins show strong lytic activity, which leads to a significantly decreased capture efficiency to the bacterial cells in short time.…”

Section: ■ Introductionmentioning

confidence: 99%

“…On the cellular surface of Gram-negative pathogens, many proteins, oligosaccharides, and lipopolysaccharides (LPSs) are capable of acting as the binding receptors for lytic phages. , Lytic phages can attach to some non-host bacteria but not cleave them because their high specificity to the host bacteria may be due to the progeny biosynthesis phase rather than the adsorption phase. Thus, the phage tail fiber protein shows a wider host spectrum than the lytic phages because phage infection requires more complex steps . It has been reported that the phage tail spike protein and endolysin have been used as molecular recognition probes for the detection of pathogenic bacteria. , However, both the proteins show strong lytic activity, which leads to a significantly decreased capture efficiency to the bacterial cells in short time.…”

Section: Introductionmentioning

confidence: 99%

Engineering Phage Tail Fiber Protein as a Wide-Spectrum Probe for Acinetobacter baumannii Strains with a Recognition Rate of 100%

et al. 2022

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As a multidrug-resistant pathogen, Acinetobacter baumannii has long been identified as one of the most common nosocomial bacteria. High-performance recognition probes for wide-spectrum detection of A. baumannii are highly desired to achieve efficient diagnosis and timely treatment of infectious diseases induced by this pathogen. An engineering tail fiber protein (ETFP) named as Gp50 encoded by lytic phage Abp9 was expressed in Escherichia coli and identified as a binding protein for A. baumannii. According to the results of genome sequencing of an A. baumannii wild strain and phage-resistant strains, the binding receptor of ETFP Gp50 is inferred to be a lipopolysaccharide distributed on the bacterial surface. The engineering protein did not show lytic activity to A. baumannii, which facilitates the development of reliable diagnosis kits and biosensors with high flexibility and low false-negative rate. The results of specificity study show that ETFP Gp50 is a species-specific binding protein with a recognition rate of 100% for all tested 77 A. baumannii strains, while that of the natural phage Abp9 is only 27.3%. With the engineering protein, a fluorescence method was developed to detect A. baumannii with a detection range of 2.0 × 10 2 to 2.0 × 10 8 cfu mL −1 . The method has been used for the quantification of A. baumannii in a diverse sample matrix with acceptable reliability. The work demonstrates the application potential of ETFP Gp50 as an ideal recognition probe for rapid screening of A. baumannii strains in a complicated sample matrix.

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“…Most phages were found to have a typical organization of the genome in functional modules, as previously described (2, 51, 52). By contrast, members of the Myoviridae family, which are included in the “larger phages” (> 100 bp), did not present specific lysis blocks, and structural and morphogenesis-related proteins were repeated in several blocks throughout the genome (38, 53). The genomes of all phages had endolysins and holins, proteins that are responsible for degradation of the bacterial cell wall during the infection by the host to facilitate the exit of the phage progeny (54).…”

Section: Discussionmentioning

confidence: 97%

Molecular analysis of the interactions between phages and the bacterial host Klebsiella pneumoniae

Bleriot

Blasco

Pacios

et al. 2022

Preprint

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Lytic phages are currently considered among the best options for treating infections caused by multi-drug resistant pathogens. Phages have some advantages over conventional antibiotics. For example, phages acquire modifications in accordance with their environment, and thus with the bacteria present, which has led to the co-evolution of both types of organism. Therefore, both phages and bacteria have acquired resistance mechanisms for protection. In this context, the aims of the present study were to analyze the proteins isolated from twenty-one novel lytic phages of Klebsiella pneumoniae in search of defence mechanisms against bacteria and also to determine the infective capacity of the phages. A proteomic study was also conducted to investigate the defence mechanisms of two clinical isolates of Klebsiella pneumoniae infected by phages. For this purpose, the twenty-one lytic phages were sequenced and de novo assembled using the Illumina-Miseq system and Spades V.3.15.2 respectively. Gene annotation was performed with Patric, Blast, Hhmer and Hhpred tools. The evolutionary relationships between phages were determined by RaxML. The host-range was determined in a collection of forty-seven clinical isolates of K. pneumoniae, revealing the variable infectivity capacity of the phages. Genome sequencing showed that all of the phages were lytic phages belonging to the family Caudovirales. The size and GC content of the phages ranged from 39,371 to 178,532 bp and from 41.72 % to 53.76 %, respectively. Phage sequence analysis revealed that the proteins were organized in functional modules within the genome. Although most of the proteins have unknown functions, multiple proteins were associated with defence mechanisms against bacteria, including the restriction-modification (RM) system, the toxin-antitoxin (TA) system, evasion of DNA degradation, blocking of host RM, the orphan CRISPR-Cas system and the anti-CRISPR system. Proteomic study of the phage-host interactions (i.e. between isolates K3574 and K3320, which have intact CRISPR-Cas systems, and phages vB_KpnS-VAC35 and vB_KpnM-VAC36, respectively) revealed the presence of several defence mechanisms against phage infection (prophage, plasmid, defence/virulence/resistance and oxidative stress proteins) in the bacteria, and of the Acr candidate (anti-CRISPR protein) in the phages.

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Exploitation of a Klebsiella Bacteriophage Receptor-Binding Protein as a Superior Biorecognition Molecule

Cited by 20 publications

References 86 publications

Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13

Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13

Engineering Phage Tail Fiber Protein as a Wide-Spectrum Probe for Acinetobacter baumannii Strains with a Recognition Rate of 100%

Molecular analysis of the interactions between phages and the bacterial host Klebsiella pneumoniae

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