Abstract
The evolutionary stability of temperate bacteriophages at low abundance of susceptible bacterial hosts lies in the trade-off between the maximization of phage replication, performed by the host-destructive lytic cycle, and the protection of the phage-host collective, enacted by lysogeny. Upon Bacillus infection, Bacillus phages phi3T rely on the “arbitrium” quorum sensing (QS) system to communicate on their population density in order to orchestrate the lysis-to-lysogeny transition. At high phage densities, where there may be limited host cells to infect, lysogeny is induced to preserve chances of phage survival. Here, we report the presence of an additional, host-derived QS system in the phi3T genome, making it the first known virus with two communication systems. Specifically, this additional system, coined “Rapφ-Phrφ”, is predicted to downregulate host defense mechanisms during the viral infection, but only upon stress or high abundance of Bacillus cells and at low density of population of the phi3T phages. Post-lysogenization, Rapφ-Phrφ is also predicted to provide the lysogenized bacteria with an immediate fitness advantage: delaying the costly production of public goods while nonetheless benefiting from the public goods produced by other non-lysogenized Bacillus bacteria. The discovered “Rapφ-Phrφ” QS system hence provides novel mechanistic insights into how phage communication systems could contribute to the phage-host evolutionary stability.
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Introduction
Temperate bacteriophages are viruses that can infect their bacterial hosts either through the host-destructive lytic cycle or the non-destructive lysogenic cycle. During the latter stage, the phage replicates as part of the bacterial genome as a “prophage” and confers immunity to a second infection upon the lysogenized bacterium [1, 2]. Lysogeny, therefore, is a strategy that protects the phage-host collective [3].
Remarkably, Erez et al. observed that upon Bacillus subtilis infection, Bacillus phage phi3T (phi3T) relies on an endogenous quorum sensing (QS) system called “arbitrium” to orchestrate the lysis-to-lysogeny transition, when phages become abundant and the susceptible hosts left to infect are likely to be few [4].
Here, we report the discovery of a second communication system, termed “Rapφ-Phrφ”, in the genome of phi3T, now the first known virus with two communication systems. Rapφ-Phrφ is the first known phage-encoded QS system predicted to regulate bacterial mechanisms, and in both a phage- and a host-density dependent manner.
Results and discussion
In addition to arbitrium, we report that Bacillus phage phi3T encodes a second QS system, coined “Rapφ–Phrφ”, from the Rap-Phr family of Bacillus bacteria [5, 6] (Fig. 1a). The Rapφ intracellular QS receptor (NCBI accession APD21157.1) is a 379aa long protein that shows 48% sequence identity over its entire length with RapC, a well-characterized member of the Rap protein family [7, 8] (Fig. 1b). Rapφ harbors tetratricopeptide repeats (TPR) (Pfam PF13181.6 and PF13424.6 HMM profiles), typically involved in the binding of QS peptides [9] (Fig. 1b). Phrφ (NCBI accession APD21156.1) is a 58aa long protein that exhibits all the characteristics of Rap cognate Phr pre-pro-peptides [10], both in terms of sequence composition (Fig. 1c) and genetic organization, with the phr gene directly downstream of rap, on the same DNA strand (Fig. 1a). Phrφ is predicted to be secreted via the SEC-translocon by SignalP-5.0 [11] (likelihood of 0.76) and harbors two characteristic regions that might be processed by extracellular proteases into the mature R-R-G-H-T and/or S-R-G-H-T QS signal pentapeptide(s) (Fig. 1c). Although non-canonical, the presence of two regions that are eventually matured into QS peptides was reported in many other functional Phr proteins [5]. The rapφ-phrφ locus forms an operon, directly flanked downstream and upstream by intrinsic terminators (Table S1). The mapping of RNA-seq reads sequenced during the infection of Bacillus by phi3T [4] to the phi3T genome indicated that rapφ and phrφ are expressed upon Bacillus infection (Fig. S1).
In the Bacillus genus, Rap-Phr systems are diverse, often strain specific and subject to horizontal transfers [5, 6]. We identified 2360 homologs of the Rapφ-Phrφ QS systems in the complete genomes of Firmicutes available on the NCBI, including 333 predicted by Phaster [12] to belong to prophages, suggesting that rap-phr QS systems are widely used and horizontally transferred by phages (Table S2 and Fig. S2). Two of the QS systems carried by prophages (RapBA3-PhrBA3 in B. velezensis FZB42 and RapBL5-PhrBL5 in B. licheniformis ATCC14580) have previously been functionally tested via a dedicated synthetic construct in B. subtilis strain PY79 (although it was then unknown that these systems belong to prophages) [5].
At low densities of the Bacillus subpopulation that either expresses the cloned rapBA3 or rapBA5 receptors, the Rap protein was experimentally demonstrated to strongly inhibit the Spo0F-P and ComA-P response regulators [5]. The Spo0F-P pathway leads to biofilm formation or sporulation [13, 14], shown to elicit the lytic cycle of certain bacteriophages [15, 16]. The ComA-P pathway triggers competence and the production of antimicrobials [17] that might contribute to the defense against phages. As a Rap-Phr expressing Bacillus subpopulation grows, the secreted Phrmature peptide accumulates in the medium. At high concentrations, PhrBA3mature and PhrBL5mature are internalized by the Opp permease and demonstrably sequester their cognate Rap receptor, which, in turn, alleviates the inhibition of ComA-P, Spo0F-P and their target pathways [5]. Therefore, there is evidence that Rap-Phr systems of prophages can delay, in Bacillus, defense mechanisms (antimicrobials, sporulation) and the production of public goods (biofilm molecules, antimicrobials) until the Bacillus subpopulation expressing the prophage QS system reaches a substantial cellular density (Figs. 2a and S3). Importantly, Rapφ-Phrφ is highly similar to RapBA3-PhrBA3. Rapφ and RapBA3 yield 77% sequence identity at full mutual coverage and harbor the exact same residues that account for the QS peptide specificity (Fig. 1b). Consistently, Phrφ presents a mature peptide region (R-R-G-H-T), identical to the PhrBA3mature QS peptide shown to inhibit RapBA3 [5] (Fig. 1c).
On these bases, we predict that Rapφ-Phrφ is likely to be functional and that Rapφ can thus downregulate host defense mechanisms via Spo0F-P and ComA-P inhibition, enhancing the efficiency of the phi3T lytic cycle. Importantly, Rapφ regulation of host processes is predicted to occur only at low concentrations of Phrφmature and when Spo0F is phosphorylated upon stress or ComA during the QS response of the entire, mixed population of Bacillus cells [13, 18, 19] (see refs. [20,21,22,23] for the potential advantages for a phage to inhibit the host’s QS response) (Figs. 2 and S4). Hence, when defense pathways are triggered at high densities of Bacillus bacteria, phi3T phages might “disarm” their host only at low densities of phages, when the phage-host collective is not yet endangered. Meanwhile, the arbitrium system of phi3T ensures a fast-replication through the lytic cycle when phages are rare. When phages become abundant, it triggers a population-wide, host-protective lysogeny [4]. Particularly, if the quorum mediated by arbitrium were reached before that of Phrφmature, the Rapφ protein of phi3T prophages could delay the production of public goods in their freshly lysogenized hosts until the lysogenized subpopulation, likely afflicted by the previous lytic cycle, reaches a substantial density [19]. Rapφ-Phrφ could hence momentarily turn lysogenized Bacillus bacteria into cheaters, enhancing both the fitness of these cells and of the phi3T prophages. Interestingly, one prophage of B. velezensis SQR9 carried both the arbitrium and the Rap-Phr QS systems, as in phi3T (Fig. S2B), further supporting that owning both communication systems might be advantageous for a temperate bacteriophage.
Data availability
All data generated or analyzed during this study are included in this published article and its Supplementary information files. The genome of Bacillus phage phi3T can be accessed from the NCBI “Assembly” database with the “ASM260144v1” accession ID. The accession IDs for the protein sequences of Rapφ and Phrφ are “APD21157.1” and “APD21156.1”, respectively.
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We would like to thank A. K. Watson for critical reading and discussion.
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C.B., Y.L., E.B., and P.L. conceived the study. C.B. performed the analyses. C.B., Y.L., and E.B. wrote the paper with input from all authors. All documents were edited and approved by all authors.
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Bernard, C., Li, Y., Lopez, P. et al. Beyond arbitrium: identification of a second communication system in Bacillus phage phi3T that may regulate host defense mechanisms. ISME J 15, 545–549 (2021). https://doi.org/10.1038/s41396-020-00795-9
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DOI: https://doi.org/10.1038/s41396-020-00795-9