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Cellulophaga Bacteriophage - Multiple mechanisms drive phage infection efficiency in nearly identical hosts

ABSTRACT: Comparison of bacteria grown with phage that are specific or non-specific for the host

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Cellulophaga Baltica Nn016038

SUBMITTER: Matthew Monroe

LAB HEAD: Matthew Sullivan

PROVIDER: PXD005440 | Pride | 2018-10-22

REPOSITORIES: Pride

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			Action	DRS
	CBT_MS_H18_iTRAQ_R1_01_29Sep14_Pippin_13-04-12.mgf	Mgf
	CBT_MS_H18_iTRAQ_R1_01_29Sep14_Pippin_13-04-12.pride.mgf.gz	Mgf
	CBT_MS_H18_iTRAQ_R1_01_29Sep14_Pippin_13-04-12.raw	Raw
	CBT_MS_H18_iTRAQ_R1_01_29Sep14_Pippin_13-04-12_msgfplus.mzid.gz	Mzid
	CBT_MS_H18_iTRAQ_R1_01_29Sep14_Pippin_13-04-12_msgfplus.pride.mztab.gz	Mztab

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Multiple mechanisms drive phage infection efficiency in nearly identical hosts.

Howard-Varona Cristina C Hargreaves Katherine R KR Solonenko Natalie E NE Markillie Lye Meng LM White Richard Allen RA Brewer Heather M HM Ansong Charles C Orr Galya G Adkins Joshua N JN Sullivan Matthew B MB

The ISME journal 20180322 6

Phage-host interactions are critical to ecology, evolution, and biotechnology. Central to those is infection efficiency, which remains poorly understood, particularly in nature. Here we apply genome-wide transcriptomics and proteomics to investigate infection efficiency in nature's own experiment: two nearly identical (genetically and physiologically) Bacteroidetes bacterial strains (host18 and host38) that are genetically intractable, but environmentally important, where phage infection efficie ...[more]

PMID: 29568113

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Multiple mechanisms drive phage infection efficiency in nearly identical hosts.

Project description:Phage-host interactions are critical to ecology, evolution, and biotechnology. Central to those is infection efficiency, which remains poorly understood, particularly in nature. Here we apply genome-wide transcriptomics and proteomics to investigate infection efficiency in nature's own experiment: two nearly identical (genetically and physiologically) Bacteroidetes bacterial strains (host18 and host38) that are genetically intractable, but environmentally important, where phage infection efficiency varies. On host18, specialist phage phi18:3 infects efficiently, whereas generalist phi38:1 infects inefficiently. On host38, only phi38:1 infects, and efficiently. Overall, phi18:3 globally repressed host18's transcriptome and proteome, expressed genes that likely evaded host restriction/modification (R/M) defenses and controlled its metabolism, and synchronized phage transcription with translation. In contrast, phi38:1 failed to repress host18's transcriptome and proteome, did not evade host R/M defenses or express genes for metabolism control, did not synchronize transcripts with proteins and its protein abundances were likely targeted by host proteases. However, on host38, phi38:1 globally repressed host transcriptome and proteome, synchronized phage transcription with translation, and infected host38 efficiently. Together these findings reveal multiple infection inefficiencies. While this contrasts the single mechanisms often revealed in laboratory mutant studies, it likely better reflects the phage-host interaction dynamics that occur in nature.

| S-EPMC5955906 | biostudies-literature

Global transcriptomic analysis of bacteriophage-host interactions between Kayvirus therapeutic phage and Staphylococcus aureus

Project description:We analyzed RNA-Seq data of two Staphylococcus aureus strains, Newman and SH1000, infected by Kayvirus phage K. Staphylococcus virus K is used in the phage therapy, its genome is 148 kb long consisting of dsDNA with long terminal repeats, and encodes 233 ORFs and 4 tRNAs. The sampling times 0, 2, 5, 10, 20, and 30 minutes after infection were chosen based on the growth characteristics of the phage K at the two S. aureus strains. From the RNA-Seq data we determined transcriptional profile of the phage K and its hosts, which allowed us to identify differentially expressed genes, ncRNAs, and promotor and terminator sites. Transcription of the phage K genes starts immediately after the infection of bacterial cells and we found a gradual take-over by phage K transcripts in the infected cells. The temporal transcriptional profile of phage K was similar in both strains and the relative expression of phage K genes shows three distinct transcript types – early, middle, and late based on the time they reach maximum expression. The bacterial response to phage K infection is similar to the general stress response. It includes the upregulation of nucleotide, amino acid and energy synthesis and transporter genes and the downregulation of transcription factors. The expression of particular virulence genes involved in adhesion and immune system evasion as well as prophage integrases were marginally affected. This work unveils the versatile nature of phage K infection leading to its broad host range

2022-03-23 | GSE190637 | GEO

Spatially resolved proteome profiling of less than 200 cells from tomato fruit pericarp by integrating laser-capture microdissection with nanodroplet sample preparation

Project description:Proteomic data from technical developments of a nanoPOTS-based spatially resolved proteome profiling of <200 cells from tomato fruit pericarp.

2018-08-21 | PXD010806 | Pride

Multifunctional Activity-Based Protein Profiling of the Developing Lung

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Gut anatomical development and microbial functional assembly of wood-feeding beetles

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Project description:Quantitative proteome analysis of progressive phycobilisome mutant variants CB, CK, and PAL to understand systematic alterations in protein expression profiles.

2017-03-09 | PXD003023 | Pride

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Project description:Comparison of the Campylobacter jejuni NCTC 11168 proteome in MH media in the presence and absence of Deoxycholate

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Evaluation of preservation quality and viability of FFPE ovarian cancer tissue samples

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Chemical profiling of live cell temporal redox dynamics in a photoautotrophic cyanobacterium

Project description:We have developed a quantitative chemical probe approach for live cell labeling of proteins that are sensitive to redox modifications. We utilize this in vivo strategy coupled to mass spectrometry-based proteomics to identify 176 proteins undergoing ~5-10 fold dynamic redox change in response to nutrient limitation and subsequent replenishment in the photoautotrophic cyanobacterium, Synechococcus sp. PCC 7002. This method enables the identification of redox changes in as little as 30 seconds after nutrient perturbation, and oscillations in reduction and oxidation for 60 minutes following the perturbation. The redox changes were validated by demonstrating that protein abundances did not change per global proteomic analyses. Peptides identified by MS for global and probe-labeled samples were required to be at least six amino acids in length having a mass spectra generating function score of <=1E-10, which corresponds to an FDR of <1%. Additionally, only peptides unique in identifying a single protein were utilized to estimate protein abundances, and proteins represented by <2 unique peptides were removed. This resulted in the identification of 176 redox probe labeled protein identifications, and 808 protein identifications in the global data.

2015-08-24 | PXD000329 | Pride

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