Evolution of Superinfection Immunity in Cluster A Mycobacteriophages

Abstract

Temperate phages encode an immunity system to control lytic gene expression during lysogeny. This gene regulatory circuit consists of multiple interacting genetic elements, and although it is essential for controlling phage growth, it is subject to conflicting evolutionary pressures. During superinfection of a lysogen, the prophage’s circuit interacts with the superinfecting phage’s circuit and prevents lytic growth if the two circuits are closely related. The circuitry is advantageous since it provides the prophage with a defense mechanism, but the circuitry is also disadvantageous since it limits the phage’s host range during superinfection. Evolutionarily related phages have divergent, orthogonal immunity systems that no longer interact and are heteroimmune, but we do not understand how immunity systems evolve new specificities. Here, we use a group of Cluster A mycobacteriophages that exhibit a spectrum of genetic diversity to examine how immunity system evolution impacts superinfection immunity. We show that phages with mesotypic (i.e., genetically related but distinct) immunity systems exhibit asymmetric and incomplete superinfection phenotypes. They form complex immunity networks instead of well-defined immunity groups, and mutations conferring escape (i.e., virulence) from homotypic or mesotypic immunity have various escape specificities. Thus, virulence and the evolution of new immune specificities are shaped by interactions with homotypic and mesotypic immunity systems. IMPORTANCE Many aspects regarding superinfection, immunity, virulence, and the evolution of immune specificities are poorly understood due to the lack of large collections of isolated and sequenced phages with a spectrum of genetic diversity. Using a genetically diverse collection of Cluster A phages, we show that the classical and relatively straightforward patterns of homoimmunity, heteroimmunity, and virulence result from interactions between homotypic and heterotypic phages at the extreme edges of an evolutionary continuum of immune specificities. Genetic interactions between mesotypic phages result in more complex mesoimmunity phenotypes and virulence profiles. These results highlight that the evolution of immune specificities can be shaped by homotypic and mesotypic interactions and may be more dynamic than previously considered.

Phage and bacteria diversification through a prophage acquisition ratchet

“…Prophages provide multiple positive attributes to the host (Brüssow et al 2004; Howard-Varona et al 2017). They confer immunity to the host cell against similar and dissimilar phages— superinfection exclusion mechanism—without necessarily compromising the host’s fitness in laboratory experiments (Bondy-Denomy et al 2016; Mavrich and Hatfull 2019). They can also provide metabolic pathways that improve the host’s competitive edge in different conditions (Bossi et al 2003; Edlin et al 1975, 1977), supply regulatory proteins (Paul 2008), and promote the expression of promiscuous bacterial enzymes (Hultqvist et al 2018).…”

Genetically similar temperate phages form coalitions with their shared host that lead to niche-specific fitness effects

“…Thus, differences in the primary sequence of the ɸ-A and ɸ-D tail fiber proteins may indicate distinct cell-surface targets for each of these phages. Furthermore, the putative transcriptional regulatory proteins encoded on ɸ-A and ɸ-D map to broad, but distinct, protein families indicating a likelihood for genotypicphenotypic mismatching [i.e., development of immunity groups; e.g., [52][53][54] leading to the observed symmetrical infection profiles.…”

Protein-Mediated and RNA-Based Origins of Replication of Extrachromosomal Mycobacterial Prophages

“…Compatibility of prophage origins. An M. smegmatis mc 2 155 lysogen of Et2Brutus was described previously (42) and lysogens of LeBron and Miko were made following the same protocol. Electrocompetent cells of the LeBron, Miko, and Et2Brutus lysogens were transformed with plasmids pJV39, pCCK38, pKSW52, pKSW09, pHA08, and pKZ07.…”

“…Nonetheless, it is surprising that many of these phage-derived plasmids are not well-maintained even with inclusion of the parABS cassette ( Table 5). Although additional regulation through the phage repressor, which is encoded by an unlinked gene, is a possibility, we note that the replication/partitioning regions are largely devoid of predicted repressor binding sites; only Rachaly and Jeeves have such sites within or flanking parABS (42). Because vector context appears to be important, as illustrated by the behaviors of RedRock-derived plasmids (see above), stabilities and copy numbers of the recombinant plasmids may not fully reflect their parent prophages.…”