Proteomic Study of the Interactions between Phages and the Bacterial Host
            <i>Klebsiella pneumoniae</i>

Bleriot, Inés; Blasco, Lucía; Pacios, Olga; Fernández‐García, Laura; López, María; Ortiz-Cartagena, Concha; Barrio-Pujante, Antonio; Fernández-Cuenca, Felipe; Pascual, Álvaro; Martı́nez-Martı́nez, Luis; Oteo, Jesús; Tomás, María

doi:10.1128/spectrum.03974-22

Cited by 14 publications

(12 citation statements)

References 75 publications

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“…K. pneumoniae strain obtain from blood infection 18 was infected with DNA lytic phage vB_KpnP-VAC25 3 at MOI 0.01, washed with PBS, and contacted with 10 MIC colistin (10 μg/mL) or 5 MIC mitomycin C (10 μg/mL). P. aeruginosa PAO1 from the Gloria Soberón collection at UNAM was infected with phage PaMx12 (DNA lytic phage, sequence https://www.ncbi.nlm.nih.gov/nuccore/386649691) at MOI 1 and surviving colonies in the center of the plaques were isolated after 20 h and tested for phage sensitivity to determine if the cells were resistant or persistent to phage.…”

Section: Methodsmentioning

confidence: 99%

Phages Produce Persisters

Fernández-García,

Kirigo,

Huelgas-Méndez

et al. 2023

Preprint

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Bacteria primarily encounter stress, and, arguably, their greatest threats are phages. It is often assumed that those bacteria that escape phage attack have mutated; however, another possibility is that a subpopulation forms the dormant persister state, in a manner similar to that demonstrated for bacterial cells undergoing nutritive, oxidative, and antibiotic stress. Persister cells do not undergo mutation and survive lethal conditions by ceasing growth transiently. Slower growth and dormancy play a key physiological role as they allow host phage defense systems more time to clear the phage infection. Here we investigated how bacteria survive lytic phage infection by isolating surviving cells from the plaques of T2, T4, and lambda (cI mutant) virulent phages. We found that bacteria in plaques can escape phage attack both by mutation (i.e., become resistant) and without mutation (i.e., become persistent). Specifically, whereas T4-resistant and lambda-resistant bacteria with over a 100,000-fold less sensitivity were isolated from plaques with obvious genetic mutations (e.g., causing mucoidy), cells were also found after T2 infection that undergo no significant mutation, retain wild-type phage sensitivity, and survive lethal doses of antibiotics. Corroborating this, adding T2 phage to persister cells resulted in 137,000-fold more survival compared to that of addition to exponentially-growing cells. Phage treatments with Klebsiella pneumonia and Pseudomonas aeruginosa also generated persister cells. Hence, along with resistant strains, bacteria also form persister cells during phage infection.

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Section: Methodsmentioning

confidence: 99%

Phages Produce Persisters

Fernández-García,

Kirigo,

Huelgas-Méndez

et al. 2023

Preprint

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“…Two K. pneumoniae lytic phages were employed: the vB_KpnM_VAC36 phage (VAC36) (Family Myoviridae , Genus Marfavirus ) and the vB_KpnM_VAC66 phage (VAC66) (Family Myoviridae , Genus Slopekvirus ) (23). Both phage genomes, VAC36 (Genbank SAMN20298872) and VAC66 (Genbank SAMN22059211) are available from the GenBank Bioproject PRJNA739095.…”

Section: Methodsmentioning

confidence: 99%

«Control of the phage defense mechanism by Quorum Sensing (QS) in clinical isolates ofKlebsiella pneumoniae»

Barrio-Pujante,

Bleriot,

Blasco

et al. 2023

Preprint

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Multidrug resistant (MDR) bacteria and the shortage of new antibiotics are a serious health problem and have increased the interest in bacteriophages, with great potential as antimicrobial agents but they can induce resistance. The objective of the present study was to reduce the development of phage resistance inK. pneumoniaestrains by inhibiting the Quorum Sensing (QS). The QS inhibition by cinnamaldehyde (CAD) was confirmed indirectly by the reduction of biofilm production and directly by a proteomic analysis. Also, the infection assays showed that the phage resistance mechanisms of the bacteria were inhibited when phage-resistantK. pneumoniaestrains were treated with a combination of phages with CAD. Finally, these results were confirmed by proteomic analysis as proteins related to the phage defence such as CBASS (bacterial cyclic oligonucleotide-based anti-phage signalling) and R-M systems as well as tail fiber proteins were present under phage treatment but not with the combination.GRAPHICAL ABSTRACT

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“…The EE09 genome was arranged in functional modules, grouping genes encoding for proteins involved in genome replication, structural conformation of viral particles (structural genes), cell lysis, and lysogenesis, as performed for other phages (Figure 2) [21]. We identified 69 coding sequences (CDS) and predicted 11 of them to encode proteins involved in phage replication (e.g., DNA polymerases), 17 to encode structural proteins (e.g., major capsid, tail proteins), 4 to be involved in host lysis (e.g., holins and lysins), 1 to participate in lysogenesis (e.g., super-infection exclusion protein).…”

Section: Characterization Of Escherichia Phage Vb_ecos-ee09mentioning

confidence: 99%

“…For example, integrating metagenomics and metaproteomics permitted the functional annotation of unknown proteins of the viral dark matter [18]. Moreover, proteomics coupled with other omics approaches unveiled the link between transcription and translation processes and phage infection efficiencies [19], helped gain insights into phage-mediated host metabolic reprogramming [20], and detected novel phage and bacterial defense mechanisms [21]. Therefore, recent evidence indicates that the combination of phage characterization with proteomics will contribute to a more profound understanding of phage-host interactions.…”

Section: Introductionmentioning

confidence: 99%

Characterization of phage vB_EcoS-EE09 infecting E. coli DSM613 Isolated from Wastewater Treatment Plant Effluent and Comparative Proteomics of the Infected and Non-Infected Host

Barrero-Canosa,

Wang,

Oyugi

et al. 2023

Microorganisms

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Phages influence microbial communities, can be applied in phage therapy, or may serve as bioindicators, e.g., in (waste)water management. We here characterized the Escherichia phage vB_EcoS-EE09 isolated from an urban wastewater treatment plant effluent. Phage vB_EcoS-EE09 belongs to the genus Dhillonvirus, class Caudoviricetes. It has an icosahedral capsid with a long non-contractile tail and a dsDNA genome with an approximate size of 44 kb and a 54.6% GC content. Phage vB_EcoS-EE09 infected 12 out of the 17 E. coli strains tested. We identified 16 structural phage proteins, including the major capsid protein, in cell-free lysates by protein mass spectrometry. Comparative proteomics of protein extracts of infected E. coli cells revealed that proteins involved in amino acid and protein metabolism were more abundant in infected compared to non-infected cells. Among the proteins involved in the stress response, 74% were less abundant in the infected cultures compared to the non-infected controls, with six proteins showing significant less abundance. Repressing the expression of these proteins may be a phage strategy to evade host defense mechanisms. Our results contribute to diversifying phage collections, identifying structural proteins to enable better reliability in annotating taxonomically related phage genomes, and understanding phage–host interactions at the protein level.

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Proteomic Study of the Interactions between Phages and the Bacterial Host Klebsiella pneumoniae

Cited by 14 publications

References 75 publications

Phages Produce Persisters

Phages Produce Persisters

«Control of the phage defense mechanism by Quorum Sensing (QS) in clinical isolates ofKlebsiella pneumoniae»

Characterization of phage vB_EcoS-EE09 infecting E. coli DSM613 Isolated from Wastewater Treatment Plant Effluent and Comparative Proteomics of the Infected and Non-Infected Host

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