Multiple mechanisms drive phage infection efficiency in nearly identical hosts

Abstract

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.

Fig. 1

The C. baltica—phage model system investigated. Generalist phage phi38:1 infects more efficiently its original host of isolation (strain NN016038; “host38”) than alternative host strain #18 (“host18”). Specialist phage phi18:3 efficiently infects its original host of isolation, “host18,” and does not infect host38 [21]

Fig. 2

Infection dynamics and expression profile of phi18:3 and phi38:1 infecting C. baltica #18 (“host18”). One-step growth curve of the a efficient phi18:3 and b inefficient phi38:1 infections on host18. Represented are the average values of three biological replicates and their standard error, as well as the latent period (LP) and burst size (BS). Time 0 represents the dilution of the infection after a 15-min adsorption. Both phages express their genes in early, middle, and late categories, with highest expression at c 0, 15, and ≥30 min for phi18:3, and d 0, 20, and ≥40 min for phi38:1. The average log₂RPKM values of the genes in each category and standard deviation are represented in the graphs. Numbers of genes in each temporal category are represented in parentheses

Fig. 3

Temporal transcriptional–translational dynamics of phi18:3 and phi38:1. For each infection, three vertical graphs represent the early, middle, or late phage transcripts. In those, averaged transcript expression is graphed with the thickest line, with “n” representing how many genes were averaged. The standardized, relative protein abundances of those transcripts are individually graphed in thinner lines, and they are early, middle, late, or a variation of those. The number in each category is also represented by an “n.” Time 0 represents the dilution of the infection after a 15-min adsorption. a–c Proteins are early (35%), middle (2%), middle late (5%), or late (58%) and they largely appear after their respective a early, b middle, and c late transcripts when phi18:3 infects host18. d–f Some (14%) phage proteins are early but most (86%) are late regardless of d early, e middle, or f late transcription of their genes when phi38:1 infects host18. g–i Phage proteins are early (4%), middle (4%), middle late (51%), late (39%), or constant (1%; protein abundance does not significantly change over time; see Supplementary Dataset S1, Tab. 10) and closely follow the g early, h middle, or i late transcription of their genes when phi38:1 infects host38. Calculations are in Supplementary Dataset S1

Fig. 4

Global transcriptome and proteome during C. baltica #18 (“host18”) infection with phi18:3 and phi38:1. OE over expressed, UE under expressed. a Host genes are globally UE throughout the infection with phi18:3, and OE throughout the infection with phi38:1. Represented is the fold change of gene expression between infected and uninfected cells, normalized by the fraction of infected cells. b, c Host protein abundances b significantly (t-test between 0 and 60 min, p ≤ 0.05) decrease by the end of the infection with phi18:3, and c significantly (t-test against 0 min, p ≤ 0.05) increase throughout the infection (≥120 min) with phi38:1. None of the uninfected host protein abundances significantly increase (t-test against 0 min, p > 0.05) over time. Represented in b and c is the average values of three biological replicates and standard error. Statistical analyses can be found in Supplementary Dataset S1 (Tab. 12). Time 0 represents the dilution of the infection after a 15-min adsorption

Fig. 5

Expression of host18’s restriction/modification (R/M) and translation genes in response to phi18:3 and phi38:1. OE over expressed; UE under expressed. Represented in a stacked bar graph is the fold change of expression of infected relative to uninfected cells, normalized by the fraction of infected cells. Solid bars represent the differential expression values whereas dotted bars represent the non-differentially expressed genes. a The R/M system is clearly differentially expressed in response to phi18:3; mostly OE throughout the infection; and UE occurs during middle infection with phi38:1. Host18 displays basal expression (non-differentially expressed genes) of the R/M system regardless of phage infection. b Host18 genes involved in protein translation are OE 4.5-fold (early), 1.7-fold (middle), and 1.4-fold (late) higher in response to phi18:3 than to phi38:1. The values of expression in host18 infected with phi38:1 do not significantly increase over time (t-test, p-value > 0.05; Supplementary Dataset S1 Tab. 7). Host18 displays basal expression (non-differentially expressed genes) of the translation genes regardless of phage infection. Time 0 represents the dilution of the infection after a 15-min adsorption

Fig. 6

Gene expression and protein abundance of “host18” protease ClpP during infection with phi18:3 and phi38:1. a The gene is only differentially expressed, and under expressed (UE), upon phi18:3 infection. Protein abundance over time during b phi18:3 infection decreases significantly (t-test, p ≤ 0.05), but during c phi38:1 infection increases significantly (t-test, p ≤ 0.05). The abundances in the controls b, c are not statistically significantly different from time 0 (t-test, p > 0.05), unlike in the infected treatment. Represented in b, c are the average of three biological replicates and their standard error. The t-tests can be found in Supplementary Dataset S1 (Tab. 7). Time 0 represents the dilution of the infection after a 15-min adsorption