Phage-Associated Mutator Phenotype in Group A Streptococcus

Abstract

Defects in DNA mismatch repair (MMR) occur frequently in natural populations of pathogenic and commensal bacteria, resulting in a mutator phenotype. We identified a unique genetic element in Streptococcus pyogenes strain SF370 that controls MMR via a dynamic process of prophage excision and reintegration in response to growth. In S. pyogenes, mutS and mutL are organized on a polycistronic mRNA under control of a common promoter. Prophage SF370.4 is integrated between the two genes, blocking expression of the downstream gene (mutL) and resulting in a mutator phenotype. However, in rapidly growing cells the prophage excises and replicates as an episome, allowing mutL to be expressed. Excision of prophage SF370.4 and expression of MutL mRNA occur simultaneously during early logarithmic growth when cell densities are low; this brief window of MutL gene expression ends as the cell density increases. However, detectable amounts of MutL protein remain in the cell until the onset of stationary phase. Thus, MMR in S. pyogenes SF370 is functional in exponentially growing cells but defective when resources are limiting. The presence of a prophage integrated into the 5 end of mutL correlates with a mutator phenotype (10 ؊7 to 10 ؊8 mutation/generation, an approximately a 100-fold increase in the rate of spontaneous mutation compared with prophage-free strains [10 ؊9 to 10 ؊10 mutation/generation]). Such genetic elements may be common in S. pyogenes since 6 of 13 completed genomes have related prophages, and a survey of 100 strains found that about 20% of them are positive for phages occupying the SF370.4 attP site. The dynamic control of a major DNA repair system by a bacteriophage is a novel method for achieving the mutator phenotype and may allow the organism to respond rapidly to a changing environment while minimizing the risks associated with long-term hypermutability.

Generation of Metabolically Diverse Strains ofStreptococcus pyogenesduring Survival in Stationary Phase

“…In the present study, sequencing of nine regulator genes of survivor strains revealed two unique mutations, a point mutation and an insertion, in two different survivor strains. Since the mutations observed in our studies occurred in late stationary phase, it is possible that the bacteria entered a hypermutable state due to stress-induced mutation or as a result of other mechanisms, such as phage inactivation of mutS (70). Diversification by random allelic mutation would result in increased fitness for the population as a whole but not necessarily for each strain generated, which is consistent with the observations that some strains, such as Alt.…”

Genomic Characterization of a Pattern D Streptococcus pyogenes emm53 Isolate Reveals a Genetic Rationale for Invasive Skin Tropicity

“…Specifically, phage ⌽AP53.5 contains only two modules, viz., lysogeny control and DNA replication, with a total length of 14.8 kb. This phage was reported to be a remnant widely present in GAS strains (36) and suffered large DNA deletions via interactions with lysogenic hosts during evolution. This phage remnant does not appear to be capable of contributing to the pathogenesis of AP53.…”

Bacterial Genome Instability

“…On the other hand, site-specific inversion systems control phase and antigenic variation independently of the cellular DNA replication, recombination, and repair pathways (see "Site-specific inversion systems," above). Similarly, ISs, prophages, and other elements, such as a plasmid containing prophage genes, induce phase variation by excision and specific reintegration (25,410,413,427) Roles of phase and antigenic variation. Most phase-and antigenic-variable proteins have important roles in mediating interactions between bacteria and their environments (393,395).…”