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Identification of proteins from SECphi18 lacking Ksap1 recognized by the KpAvs2 bacterial defense system during infection of Escherichia coli.

ABSTRACT: Antiviral STANDs (Avs) are bacterial anti-phage proteins that are considered as the evolutionary ancestors of immune pattern-recognition receptors of the NLR family. Following the recognition of a conserved phage protein, Avs proteins exhibit cellular toxicity and abort phage propagation by killing the infected cell. Type 2 Avs proteins (Avs2) were suggested to recognize the large terminase subunit of the phage by direct binding as a signature of phage infection based on co-expression assays. Here, we analyzed the binding partners of a type 2 Avs protein from Klebsiella pneumoniae (KpAvs2) expressed in Escherichia coli. Previous analysis revealed that, during phage SECphi18 infection, KpAvs2 recognized a small protein of unknown function, Ksap1. We repeated the experiment with a SECphi18 phage mutated for Ksap1 to see if KpAvs2 could recognize other proteins, such as the terminase, in absence of Ksap1.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Escherichia Coli

TISSUE(S): Cell Suspension Culture

SUBMITTER: Nathalie Bechon

LAB HEAD: Rotem Sorek

PROVIDER: PXD054784 | Pride | 2024-12-04

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	AllQuantifiedPeptides.tsv	Tabular
	AllQuantifiedProteinGroups.tsv	Tabular
	HF2_RS_21382_7-SHA-A_16052024_240517140853.raw	Raw
	HF2_RS_21382_7-SHA-B_16052024.raw	Raw
	HF2_RS_21382_7-SHA-C_16052024_240517153408.raw	Raw

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Identification of proteins from the SECphi18 bacteriophage recognized by the KpAvs2 bacterial defense system during infection of Escherichia coli.

Project description:Antiviral STANDs (Avs) are bacterial anti-phage proteins that are considered as the evolutionary ancestors of immune pattern-recognition receptors of the NLR family. Following the recognition of a conserved phage protein, Avs proteins exhibit cellular toxicity and abort phage propagation by killing the infected cell. Type 2 Avs proteins (Avs2) were suggested to recognize the large terminase subunit of the phage by direct binding as a signature of phage infection based on co-expression assays. Here, we analyzed the binding partners of a type 2 Avs protein from Klebsiella pneumoniae (KpAvs2) expressed in Escherichia coli during SECphi18 phage infection and showed that rather than the large terminase subunit, KpAvs2 binds a small phage protein of unknown function during infection.

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Project description:This dataset was created to (i) compare the protein expression of E. coli DSM613 cells infected and uninfected with phage vB_EcoS-EE09 and (ii) detect structural proteins of phage vB_EcoS-EE09. Thus, this set provides proteomic data of three setups: 1. Uninfected E. coli DSM613 (file names [file ID]: 04_22A [F40]; 13_ecolicontrol_01 [F13]; 14_ecolicontrol_02 [F14]) 2. E. coli DSM613 infected with phage vB_EcoS-EE09 (file names [file ID]: 02_13A [F39]; 27_ecoliinfected_01 [F27]; 28_ecoliinfected_02 [F28]) 3. Cell-free phage lysate of phage vB_EcoS-EE09 (sample name: 01_EE09)

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RNA-Seq analysis of Pseudomonas aeruginosa PAO1 cells infected with PhiKZ phage

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Investigating Lactococcus lactis MG1363 response to phage p2 infection at the proteome level

Project description:Phages are viruses that specifically infect and kill bacteria. Bacterial fermentation and biotechnology industries see them as enemies, however, they are also investigated for the treatment or prevention of infections caused by multidrug resistant bacteria. Whether foes or allies, their importance is undeniable. Despite decades of research some aspects of phage biology are still poorly understood. In this study, we used label-free quantitative proteomics to reveal the proteotypes of Lactococcus lactis MG1363 during infection by the virulent phage p2, a model for studying the biology of phages infecting Gram-positive bacteria. Our approach resulted in the high-confidence detection and quantification of 59% of the theoretical bacterial proteome, including 226 bacterial proteins detected only during phage infection and 6 proteins unique to uninfected bacteria. We also identified many bacterial proteins of differing abundance during the infection. Using this high-throughput proteomic datasets, we selected specific bacterial genes for inactivation using CRISPR-Cas9 to investigate their involvement in phage replication. One knockout mutant lacking gene llmg_0219 showed resistance to phage p2 due to a deficiency in phage adsorption. Furthermore, we detected and quantified 78% of the theoretical phage proteome and identified many proteins of phage p2 that had not been previously detected. Among others, we uncovered a conserved small phage protein (ORFN1) coded by an unannotated gene. We also applied a targeted approach to achieve greater sensitivity and identify undetected phage proteins that were expected to be present. This allowed us to follow the fate of ORF46, a small phage protein of low abundance. In summary, this work offers a unique view of the virulent phages’ takeover of bacterial cells and provides novel information on phage-host interactions.

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