Abstract
Streptococcus pyogenes chromosomal island M1 (SpyCIM1) integrates by site-specific recombination into the 5’ end of DNA mismatch repair (MMR) gene mutL in strain SF370SmR, blocking transcription of it and the downstream operon genes. During exponential growth, SpyCIM1 excises from the chromosome and replicates as an episome, restoring mutL transcription. This process is reversed in stationary phase with SpyCIM1 re-integrating into mutL, returning the cells to a mutator phenotype. Here we show that elimination of SpyCIM1 relieves this mutator phenotype. The downstream MMR operon genes, multidrug efflux pump lmrP, Holliday junction resolution helicase ruvA, and DNA base excision repair glycosylase tag, are also restored to constitutive expression by elimination of SpyCIM1. The presence of SpyCIM1 alters global transcription patterns in SF370SmR. RNA sequencing (RNA-Seq) demonstrated that loss of SpyCIM1 in the SpyCIM1 deletion mutant, CEM1Δ4, impacted the expression of over 100 genes involved in virulence and metabolism both in early exponential phase, when the SpyCIM1 is episomal, as well as at the onset of stationary phase, when SpyCIM1 has reintegrated into mutL. Among these changes, the up-regulation of the genes for the antiphagocytic M protein (emm1), streptolysin O (slo), capsule operon (hasABC), and streptococcal pyrogenic exotoxin (speB), are particularly notable. The expression pattern of the MMR operon confirmed our earlier observations that these genes are transcribed in early exponential phase but silenced as stationary phase is approached. Thus, the direct role of SpyCIM1 in causing the mutator phenotype is confirmed, and further, its influence upon the biology of S. pyogenes was found to impact multiple genes in addition to the MMR operon, which is a novel function for a mobile genetic element. We suggest that such chromosomal islands are a remarkable evolutionary adaptation to promote the survival of its S. pyogenes host cell in changing environments.
Highlights
Prophages and prophage-like elements are universal components of the genomes of Streptococcus pyogenes, with the published genome sequences having between two and eight examples in each strain [1,2,3,4,5,6,7,8,9,10,11,12]
We demonstrated that a prophage-like mobile genetic elements (MGE) in the S. pyogenes M1 genome strain SF370 acted as a genetic switch that controlled the expression of the DNA mismatch repair (MMR) gene mutL as well as additional downstream genes
DNA was isolated from cells after overnight incubation at 37°C, a condition where we previously showed that Streptococcus pyogenes chromosomal island M1 (SpyCIM1) would be integrated into the bacterial doi:10.1371/journal.pone.0145884.g001
Summary
Prophages and prophage-like elements are universal components of the genomes of Streptococcus pyogenes (group A streptococcus), with the published genome sequences having between two and eight examples in each strain [1,2,3,4,5,6,7,8,9,10,11,12]. We demonstrated that a prophage-like MGE in the S. pyogenes M1 genome strain SF370 acted as a genetic switch that controlled the expression of the DNA mismatch repair (MMR) gene mutL as well as additional downstream genes These genes are encoded on a polycistronic mRNA along with mutS, and the result of this regulation caused a growth-dependent mutator phenotype [15]. This cycle of excision and re-integration results in the cell switching between a complex mutator and normal phenotype [15] This system is remarkable in that is MMR regulated by this MGE, but it controls a multiple drug efflux pump (lmrP), a Holliday junction helicase subunit (ruvA), and a component of base excision repair (tag). We extended this original observation to demonstrate that the frequent carriage of related SpyCI elements in the genomes of other S. pyogenes strains was associated with a mutator phenotype [16]
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