Reprogramming Bacteriophage Host Range through Structure-Guided Design of Chimeric Receptor Binding Proteins

Dunne, Matthew; Rupf, Beatrice; Tala, Marc; Qabrati, Xhem; Erñst, Patrick; Shen, Yang; Sumrall, Eric T.; Heeb, Laura; Plückthun, Andreas; Loessner, Martin J.; Kilcher, Samuel

doi:10.1016/j.celrep.2019.09.062

Cited by 154 publications

(137 citation statements)

References 80 publications

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“…In addition, these methods have the capability to identify fitness costs associated with broadly seen phage resistance phenotypes in a competitive natural environment, and thus improve our understanding of microbial ecology in general [13,114,206,207,[210][211][212]. Such systems-level insights will be valuable both in uncovering new mechanisms in host-phage interaction and perhaps in developing different design strategies for targeted microbial community interventions, engineering highly virulent or extended host-range phages and rationally formulated phage-cocktails for therapeutic applications [89,204,208,[213][214][215][216][217][218][219][220][221][222][223][224][225][226]. Alternatively, identifying phage resistance determinants may also enable engineering of bacterial strains with phage defense systems crucial in a number of bioprocesses such as in the dairy industry [227,228], biocontainment strategies for bioproduction industry [229,230] or to facilitate bacterial vaccine discovery and development [231][232][233].…”

Section: Discussionmentioning

confidence: 99%

High-throughput mapping of the phage resistance landscape inE. coli

Mutalik¹,

Adler²,

Rishi³

et al. 2020

Preprint

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Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and highthroughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phagemediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.3 Introduction:

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Section: Discussionmentioning

confidence: 99%

High-throughput mapping of the phage resistance landscape inE. coli

Mutalik¹,

Adler²,

Rishi³

et al. 2020

Preprint

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“…Depending on the binding specificity of the employed viral particle, LUX-MS enables the spatiotemporal elucidation of viral attachment sites, target receptors, and global surfaceomes of live prokaryotic and eukaryotic cells in complex biological systems. This is of particular interest considering the broad application of advanced phage display assays 77 and related screening platforms 5,78 in basic and translational research. Finally, we employed LUX-MS for the spatiotemporal analysis of intercellular surfaceome signaling domains within immunological synapses.…”

Section: Discussionmentioning

confidence: 99%

“…As such, mapping ligand-targeted surfaceome landscapes with nanoscale precision should provide fundamental insights into cellular signaling function in health and disease with wide-reaching implications for the development of therapeutic strategies. Specifically, unravelling surfaceome signaling interactions in space and time would substantially advance drug development (deconvoluting drug targets and mechanism of action) and enable discoveries in broad research areas including cell biology (dissecting receptor signaling) 4 , microbiology (identifying pathogen binding sites) 5 and immunology (elucidating immunosynaptic communication) 6 .…”

Section: Introductionmentioning

confidence: 99%

Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks

Müller

Gräbnitz

Barandun

et al. 2020

Preprint

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Delineating the molecular nanoscale organization of the surfaceome is pre-requisite for understanding cellular signaling. Technologies for mapping the spatial relationships of cell surface receptors and their extracellular signaling synapses would open up theranostic opportunities and the possibility to engineer extracellular signaling. Here, we developed an optoproteomic technology termed LUX-MS that exploits singlet oxygen generators (SOG) for the light-triggered identification of acute protein interactions on living cells. Using SOG-coupled antibodies, small molecule-drugs, biologics and intact viral particles, we show that not only ligand-receptor interactions can be decoded across organisms, but also the surfaceome receptor nanoscale organization ligands engage in with direct implications for drug action. Furthermore, investigation of functional immunosynapses revealed that intercellular signaling inbetween APCs and CD8+ T cells can be mapped now providing insights into T cell activation with spatiotemporal resolution. LUX-MS based decoding of surfaceome signaling architectures provides unprecedented molecular insights for the rational development of theranostic strategies.

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“…Bacteriophages A500 and PSA possess the unique ability to adsorb to and infect serovar 4b strains (Dorscht et al, 2009;Loessner & Busse, 1990;Zink & Loessner, 1992). Deletion of gttA resulted in resistance to A500 and PSA infection, due to loss of adsorption (Dunne et al, 2019;Sumrall et al, 2019). Nevertheless, it could not be definitively concluded whether these phages utilize Gal-WTA alone as a receptor, since GttA mediates the addition of Gal to both LTA and WTA chains.…”

Section: Bacteriophages With a 4b-specific Host Range Require Only mentioning

confidence: 99%

Galactosylated wall teichoic acid, but not lipoteichoic acid, retains InlB on the surface of serovar 4b Listeria monocytogenes

Sumrall

Schefer

Rismondo

et al. 2020

Molecular Microbiology

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Listeria monocytogenes is a Gram‐positive, intracellular pathogen harboring the surface‐associated virulence factor InlB, which enables entry into certain host cells. Structurally diverse wall teichoic acids (WTAs), which can also be differentially glycosylated, determine the antigenic basis of the various Listeria serovars. WTAs have many physiological functions; they can serve as receptors for bacteriophages, and provide a substrate for binding of surface proteins such as InlB. In contrast, the membrane‐anchored lipoteichoic acids (LTAs) do not show significant variation and do not contribute to serovar determination. It was previously demonstrated that surface‐associated InlB non‐covalently adheres to both WTA and LTA, mediating its retention on the cell wall. Here, we demonstrate that in a highly virulent serovar 4b strain, two genes gtlB and gttB are responsible for galactosylation of LTA and WTA respectively. We evaluated the InlB surface retention in mutants lacking each of these two genes, and found that only galactosylated WTA is required for InlB surface presentation and function, cellular invasiveness and phage adsorption, while galactosylated LTA plays no role thereof. Our findings demonstrate that a simple pathogen‐defining serovar antigen, that mediates bacteriophage susceptibility, is necessary and sufficient to sustain the function of an important virulence factor.

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Reprogramming Bacteriophage Host Range through Structure-Guided Design of Chimeric Receptor Binding Proteins

Cited by 154 publications

References 80 publications

High-throughput mapping of the phage resistance landscape inE. coli

High-throughput mapping of the phage resistance landscape inE. coli

Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks

Galactosylated wall teichoic acid, but not lipoteichoic acid, retains InlB on the surface of serovar 4b Listeria monocytogenes

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