Characterization of the interactions between <i>Escherichia coli</i> receptors, LPS and OmpC, and bacteriophage T4 long tail fibers

Washizaki, Ayaka; Yonesaki, Tetsuro; Otsuka, Yuichi

doi:10.1002/mbo3.384

Cited by 95 publications

(114 citation statements)

References 39 publications

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“…Lack of ompC in the BL21 strain probably alleviates the need for the EnvZ/OmpR two-component system for T4 infection. The absolute requirement for LPS R-core structure for T4 phage growth on BL21 is in agreement with the earlier reports [90,93,[176][177][178]. Similarly, CEV1 phage, which showed a strict requirement for OmpF and full length LPS in K-12 screens (Fig.…”

Section: Extending Genome-wide Screens To E Coli Bl21 Strainsupporting

confidence: 92%

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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: Extending Genome-wide Screens To E Coli Bl21 Strainsupporting

confidence: 92%

“…2B), and is deficient in Lon and OmpT proteases important components of the protein homeostasis network [172][173][174]. In addition, BL21 also lacks ompC and nfrAB genes that code for T4 phage and N4 phage receptors in E. coli K-12 respectively [172,175,176].…”

Section: Extending Genome-wide Screens To E Coli Bl21 Strainmentioning

confidence: 99%

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

Mutalik¹,

Adler²,

Rishi³

et al. 2020

Preprint

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“…We thus reasoned that placing the llp gene under the control of the opvAB promoter might confer resistance to T5 only in the ON state. As expected from the literature, a Δ fhuA strain proved resistant to T5, but not to T4, which uses OmpC as receptor (51) (Fig. 7A).…”

Section: Resultssupporting

confidence: 82%

Phase variation-based biosensors for bacteriophage detection and phage receptor discrimination

Olivenza

Casadesús

Ansaldi

2019

Preprint

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13Environmental monitoring of bacteria using phage-based biosensors has been widely 14 developed for many different species. However, there are only a few available methods to 15 detect specific bacteriophages in raw environmental samples. In this work, we developed a 16 simple and efficient assay to rapidly monitor the phage content of a given sample. The assay is 17 based on the bistable expression of the Salmonella enterica opvAB operon. Under regular 18 growth conditions, opvAB is only expressed by a small fraction of the bacterial subpopulation. 19In the OpvAB ON subpopulation, synthesis of the OpvA and OpvB products shortens the O-20 antigen in the lipopolysaccharide and confers resistance to phages that use LPS as a receptor. 21As a consequence, the OpvAB ON subpopulation is selected in the presence of such phages. 22Using an opvAB::gfp fusion, we could monitor LPS-binding phages in various media, including 23 raw water samples. To enlarge our phage-biosensor panoply, we also developed several 24 coliphage biosensors that proved efficient to detect LPS-as well as protein-binding coliphages. 25Moreover, the combination of these tools allows to identify what is the bacterial receptor 26 triggering phage infection. The opvAB::gfp biosensor thus comes in different flavours to 27 efficiently detect a wide range of bacteriophages and identify the type of receptor they 28 recognize. 29 30 31 from environmental samples still constitutes a challenge for those interested in isolating and 35 characterizing bacteriophages for ecological or biotechnological purposes. This work provides 36 a simple and accurate method based on the bi-stable expression of genes that confer 37 resistance to certain classes of bacteriophages in different bacterial models. It paves the way 38 for future development of highly efficient phage biosensors that can discriminate among 39 several receptor-binding phages and that could be declined in many more versions. In a 40 context where phage ecology, research, and therapy are flourishing again, it becomes essential 41 to possess simple and efficient tools for phage detection.42 43 44 45 Keywords: bacteriophage, biosensor, phase variation, LPS, phage receptor 46 47 48 49Bacteriophages, the viruses that infect bacteria, are ubiquitous on Earth, very abundant and 50 highly diverse (1-4). They participate in the daily turnover of bacterial communities and are 51 hypothesized to be major drivers of carbon recycling (5). Their abundance and diversity have 52 long been acknowledged in the oceans and more recently associated to numerous 53 microbiomes as a major part of the viromes (2,(6)(7)(8). Bacteriophages are considered a vast 54 reservoir of genes and a major vector for horizontal gene transfer that allow the emergence of 55 new biological functions (9, 10). Furthermore, phages have been at the origin of many 56 discoveries and concepts in molecular biology (11)(12)(13). 57Among the applications resulting from a century of phage research, phage therapy stands out 58 by receiving more and more a...

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“…That is why we speculate that limitation of certain component in the medium cannot be directly responsible for observed trend but it can have an indirect impact. According to the literature, phage T4 adsorbs to the lipopolysaccharides (LPS) in the outer membrane in E. coli B/r, whereas T4 requires LPS and outer membrane porin protein C (OmpC) as well for proper phage receptor function in E. coli K‐12 (Henning & Jann, ; Rakhuba, Kolomiets, Dey, & Novik, ; Washizaki, Yonesaki, & Otsuka, ; Yu & Mizushima, ). The concentration of LPS was estimated at 10 6 monomers of LPS per bacterial cell, the same value was determined for different strains (Smit, Kamio, & Nikaido, ; Washizaki et al., ).…”

Section: Discussionmentioning

confidence: 99%

Effect of bacterial growth rate on bacteriophage population growth rate

2017

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It is important to understand how physiological state of the host influence propagation of bacteriophages (phages), due to the potential higher phage production needs in the future. In our study, we tried to elucidate the effect of bacterial growth rate on adsorption constant (δ), latent period (L), burst size (b), and bacteriophage population growth rate (λ). As a model system, a well‐studied phage T4 and Escherichia coli K‐12 as a host was used. Bacteria were grown in a continuous culture operating at dilution rates in the range between 0.06 and 0.98 hr−1. It was found that the burst size increases linearly from 8 PFU·cell−1 to 89 PFU·cell−1 with increase in bacteria growth rate. On the other hand, adsorption constant and latent period were both decreasing from 2.6∙10‐9 ml·min−1 and 80 min to reach limiting values of 0.5 × 10‐9 ml·min−1 and 27 min at higher growth rates, respectively. Both trends were mathematically described with Michaelis–Menten based type of equation and reasons for such form are discussed. By applying selected equations, a mathematical equation for prediction of bacteriophage population growth rate as a function of dilution rate was derived, reaching values around 8 hr−1 at highest dilution rate. Interestingly, almost identical description can be obtained using much simpler Monod type equation and possible reasons for this finding are discussed.

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Characterization of the interactions between Escherichia coli receptors, LPS and OmpC, and bacteriophage T4 long tail fibers

Cited by 95 publications

References 39 publications

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

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

Phase variation-based biosensors for bacteriophage detection and phage receptor discrimination

Effect of bacterial growth rate on bacteriophage population growth rate

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