Figures and data in Viral commitment to infection depends on host metabolism

Figures
Tables
Additional files

5 figures, 2 tables and 2 additional files

Figures

Figure 1 with 2 supplements

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Effect of hosts’ metabolic condition on viral commitment to infection.

(**A–E**) display the results of the Ratio, defined as $Ratio = \frac{R_{A s / A z}}{R_{G l u}}$ , where R_As/Az = (Free viral particles after mixing with bacteria in As/Az)/(Free viral particles in bacteria-free buffer with As/Az), and R_Glu = (Free viral particles after mixing with bacteria in Glu)/(Free viral particles in bacteria-free buffer with Glu). This Ratio captures how the host’s metabolic state affects viral commitment to infection, comparing energy-depleted (As/Az) with energy-competent (Glu) conditions across three experiments and their average. Each panel corresponds to a specific phage, as indicated above the respective panel. Lighter-colored bars represent data from permissive hosts, while darker-colored bars show results from resistant host controls for comparison. The red horizontal dashed line represents the scenario where $Ratio = 1$ , indicating that the number of free viral particles is the same in energy-competent and energy-depleted bacteria. The incubation time for each phage–host pair is consistent across all three experiments and is displayed in the upper-right corner of each panel. The standard error of the mean (SEM) is used to estimate the variability in the averages, accounting for the random measurement errors across the three independent experiments.

Figure 1—figure supplement 1

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Average phage counts.

(**A-E**) Each panel displays the average count of phage particles as represented by PFU per µl in the post-cellular supernatant. Yellow bars represent phages from experiments with bacteria grown in glucose, while blue bars indicate phages from bacteria grown in arsenate and azide. Each pair of bars corresponds to interactions with different bacterial types: permissive, resistant, and buffer controls. These results are also presented in the ’All Experiments Averages’ section of the tables in Supplementary file 1 – worksheets ‘Phage-specific results’ and ‘Averages’.

Figure 1—figure supplement 2

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Ratio to buffer in glucose across phages.

(**A-E**) Each panel presents the results of the negative logarithm of R_P in glucose, where R_P represents the ratio of viral counts from permissive hosts relative to the buffer control in glucose-grown bacteria. The data are organized into four columns: one for each of the three independent experiments and one for the overall average, a necessary quantity for calculating the adsorption rate η. Each panel corresponds to a different phage, as indicated above the panel. These results are also reported in the ‘All Experiments Averages’ section of the tables in Supplementary file 1 – worksheets ‘Phage-specific results’ and ‘Averages’.

Figure 2

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Comparing the metabolic condition effect on phage adsorption rate.

The y-axis of both panels represents the relative effect of growth in arsenate and azide (low metabolic condition) on the adsorption rate, $η^{'}$ , compared to the adsorption rate in the high metabolic condition, η, for hosts grown in glucose. A displays this effect for each phage (x-axis), while B illustrates the relationship between the effect and the adsorption rate in glucose, η. The dashed line in B shows an orthogonal distance regression (ODR) fit of the phages whose adsorption was affected by the host’s metabolic state (T5 was excluded because no detectable effect was observed). The relationship is modeled as $η^{'} / η = A \log_{10} (η) + B$ , with fitted parameters $A = 0.28 \pm 0.10$ and $B = 3.3 \pm 1.0$ , where the uncertainties denote standard errors of the fit. The plotted regression line uses the full-precision parameter values, while the values reported here are rounded for clarity.

Figure 3

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Schematic of the phenomenon.

This illustration compares the ability of viral particles to enter upon encountering energy-competent bacteria (yellow, left) versus energy-depleted bacteria (purple, right). The upper part depicts a sequence of events, following the arrows from left to right, showing phage behavior when encountering a high-metabolic-state (energy-competent) host versus a low-metabolic-state (energy-depleted) host. At the population level, a greater percentage of free viral particles in the buffer will commit to infecting a community of high-metabolic-state hosts (grown in glucose) compared to those at a low metabolic state (grown in arsenate and azide). Created with BioRender.com.

Figure 4

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Two-step infection dynamics with a discrimination mechanism.

After binding to a receptor at a rate $k$ , the phage can either irreversibly commit to the adsorption at a rate $k_{com}$ , or can leave again with a rate $k_{off}$ as introduced in Stent and Wollman, 1952; Schwartz, 1976; Moldovan et al., 2007. This slows down the commitment process by factor $1 / (1 + k_{off} / k_{com})$ , but opens for the discrimination between the active and inactive hosts by having different values of $k_{off} / k_{com}$ . Created with BioRender.com.

Figure 5

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The experimental protocol.

Each dot represents a step in the experimental protocol. The accompanying text below and the image above provide a detailed description of the process. The sequence of steps follows the solid line from the upper left (start) to the lower right (end), indicating the correct order. The dotted line with an arrow and the ‘x2’ marker denotes a looped process in the protocol. Created with BioRender.com.

Tables

Table 1

Adsorption rate in glucose (η) and the effect of altered metabolic conditions (growth in arsenate and azide) on it ( $η^{'} / η$ ) for different phages.

This table presents the experimentally determined adsorption rates (η) for each phage when grown in glucose, along with the relative adsorption rates ( $η^{'} / η$ ) under arsenate and azide (As/Az) conditions, reflecting the impact of altered metabolic states. In the cases of m13 and T6, the relative adsorption rate ( $η^{'} / η$ ) exhibits increased variability, with SEMs exceeding the mean values. This is due to very low adsorption under As/Az conditions, where free viral particle counts approach those of the buffer control (see Figure 1—figure supplement 1, Supplementary file 1 – worksheet ‘Averages’). While this inflates relative variability, the results remain consistent with a strong reduction in adsorption efficiency. Furthermore, corresponding literature value ranges for are included for comparison, with references provided. However, it is important to highlight that such comparisons are limited by differences in experimental protocols, host and virus strains, and growth conditions (e.g., temperature and media). Altering any of these factors has been reported to cause variations in adsorption rates, typically by up to an order of magnitude, and in some cases by even more than a 100-fold (Heller and Braun, 1979; Moldovan et al., 2007; Braun, 2009; Storms et al., 2012; Tomat et al., 2022). For example, in the case of T6, where we observe the largest discrepancy, literature values were obtained using different bacterial strains, grown in different media, at 24°C, which is 13°C lower than the 37°C temperature used in our experiments.

Phage	η (×10^–11 ml/(CFU·min))	$η^{'} / η$	Literature η (×10^–11 ml/(CFU·min))	References
λ	15.5 ± 2.7	0.53 ± 0.03	[1.3, 1100]	Hendrix and Duda, 1992; De Paepe and Taddei, 2006; Moldovan et al., 2007; Shao and Wang, 2008; Storms et al., 2012
ϕ80	1.7 ± 0.3	0.37 ± 0.05	[11, 38]	Kadner et al., 1980; De Paepe and Taddei, 2006
m13	1.32 ± 0.23	0.06 ± 0.08	[3, 9]	Tzagoloff and Pratt, 1964; De Paepe and Taddei, 2006
T6	0.32 ± 0.06	0.08 ± 0.11	[93, 340]	Storms et al., 2012
T5	5.8 ± 1.2	1.03 ± 0.16	[4, 2500]	Heller and Braun, 1979; Kadner et al., 1980; De Paepe and Taddei, 2006; Storms et al., 2012

Key resources table

Reagent type (species) or resource	Designation	Source or reference	Identifiers	Additional information
Strain, strain background (Escherichia coli K-12)	MC4100	Casadaban, 1976	N/A	F⁻araD139 Δ(argF-lac)U169 flhD5301 Δ(fruK-yeiR)725(fruA25) relA1 rpsL150 rbsR22 Δ(fimB-fimE)632::IS1 deoC1
Strain, strain background (Escherichia coli K-12)	S2153	Sneppen et al., 2023	N/A	as MC4100 but fhuA⁻
Strain, strain background (E. coli K-12)	S3190	This study	N/A	HfrH lacI^q fhuA⁻
Strain, strain background (E. coli K-12)	S3207	Sneppen et al., 2023	N/A	as S2153 but (λrex::gfp) Δ(rex-galK)::kan
Strain, strain background (E. coli K-12)	S3222	Brown et al., 2022	N/A	as S3207 but λvir^r Mal⁻
Strain, strain background (E. coli K-12)	tsx	Baba et al., 2006	KEIO JW0401-1	F⁻Δ(araD-araB)567 ΔlacZ4787(::rrnB-3) Δtsx-773::kan λ- rph-1 Δ(rhaD-rhaB)568 hsdR514
Strain, strain background (E. coli K-12)	Δxyl	Baba et al., 2006	N/A	as KEIO JW0401-1 but tsx⁺ ΔxylA::kan
Strain, strain background (bacteriophage λ)	λcIb221	Authors’ laboratory stock	N/A	λcI ET22 Δatt b221
Strain, strain background (bacteriophage ϕ80)	ϕ80vir	Authors’ laboratory stock	N/A	N/A
Strain, strain background (bacteriophage m13)	m13	Authors’ laboratory stock	N/A	N/A
Strain, strain background (bacteriophage T5)	T5	Authors’ laboratory stock	N/A	N/A
Strain, strain background (bacteriophage T6)	T6	Authors’ laboratory stock	N/A	N/A