Layers of Evolvability in a Bacteriophage Life History Trait

Abstract

Functional redundancy in genomes arises from genes with overlapping functions, allowing phenotypes to persist after gene knockouts. Evolutionary redundancy or evolvability of a genome is one step removed, in that functional redundancy is absent but the genome has the potential to evolve to restore a lost phenotype. Exploring the extent to which this recovery alters gene networks can illuminate how functional gene interactions change through time. Here, the evolvability of lysis was studied in bacteriophage T7, revealing hidden functional interactions. Lysis is the destruction of host cell wall and membranes that releases progeny and is therefore essential for phage propagation. In most phages, lysis is mediated by a two-component genetic module: a muralytic enzyme that degrades the bacterial cell wall (endolysin) and a holin that permeabilizes the inner membrane to allow the endolysin access to the cell wall. T7 carries one known holin, one endolysin, and a second muralytic enzyme that plays little role in lysis by wild-type phage. If the primary endolysin is deleted, the second muralytic enzyme evolves to restore normal lysis after selection for faster growth. Here, a second level of evolutionary redundancy was revealed. When the second muralytic enzyme was prevented from adapting in a genome lacking the primary endolysin, the phage reevolved lysis de novo in the absence of any known muralytic enzymes by changes in multiple genes outside the original lysis module. This second level of redundancy proved to be evolutionarily inferior to the first, and both result in a lower fitness and slower lysis than wild-type T7. Deletion of the holin gene delayed lysis time modestly; fitness was restored by compensatory substitutions in genes that lack known roles in lysis of the wild type.

Lysis Delay and Burst Shrinkage of Coliphage T7 by Deletion of Terminator Tφ Reversed by Deletion of Early Genes

“…Accordingly, it is suggested that some unknown factors other than holin, lysozyme, and spanins are involved in the lysis pathway of T7 phage. Heineman et al (14) also suggested that T7 contains additional holins, as their optimality failed to predict the lysis time of T7 phage.…”

“…Phage burst size was measured as previously described (14), with some modifications. Briefly, a BL21 culture at an A 595 of 0.3 to 0.4 was infected with phages at a multiplicity of infection (MOI) of 0.02.…”

Functional Analysis of the Holin-Like Proteins of Mycobacteriophage Ms6

“…Deletion of the chaperone-like protein gp1 in both deletion mutants Ms6 ⌬gp4 and Ms6 ⌬gp5 was catastrophic for lysis, with more than 3-fold reduction of the burst size, even though the mutant phage are viable and could be isolated. Remarkably, although Gp5 was unable to allow endolysin-mediated lysis in E. coli, a mutant phage lacking both gp1 and gp4 was able to infect M. smegmatis cells and undergo lysis, so it is expected that there will be alternative pathways to release phage progeny (13). We conclude that for mycobacteriophage Ms6 and related mycobacteriophages, the presence of the endolysin in addition to one of the lytic genes, gp1, gp4, or gp5, is sufficient for a lysis phenotype.…”

Tuning a Genetic Switch: Experimental Evolution and Natural Variation of Prophage Induction

“…Although essential for the establishment of lysogeny, the fact that no mutations occurred in these genes suggests that they do not participate in adaptive evolution of the decision making process. These observations follow an emerging theme in experimental studies of microbes: evolution often finds solutions other than those that are nominated a priori, despite an often very detailed knowledge of the system in question (e.g., Blount et al 2008;Beaumont et al 2009;Harris et al 2009;Heineman et al 2009;McDonald et al 2009).…”