Parallel Evolution inStreptococcus pneumoniaeBiofilms

Abstract

Streptococcus pneumoniae is a commensal human pathogen and the causative agent of various invasive and noninvasive diseases. Carriage of the pneumococcus in the nasopharynx is thought to be mediated by biofilm formation, an environment where isogenic populations frequently give rise to morphological colony variants, including small colony variant (SCV) phenotypes. We employed metabolic characterization and whole-genome sequencing of biofilm-derived S. pneumoniae serotype 22F pneumococcal SCVs to investigate diversification during biofilm formation. Phenotypic profiling revealed that SCVs exhibit reduced growth rates, reduced capsule expression, altered metabolic profiles, and increased biofilm formation compared to the ancestral strain. Whole-genome sequencing of 12 SCVs from independent biofilm experiments revealed that all SCVs studied had mutations within the DNA-directed RNA polymerase delta subunit (RpoE). Mutations included four large-scale deletions ranging from 51 to 264 bp, one insertion resulting in a coding frameshift, and seven nonsense single-nucleotide substitutions that result in a truncated gene product. This work links mutations in the rpoE gene to SCV formation and enhanced biofilm development in S. pneumoniae and therefore may have important implications for colonization, carriage, and persistence of the organism. Furthermore, recurrent mutation of the pneumococcal rpoE gene presents an unprecedented level of parallel evolution in pneumococcal biofilm development.

The ω Subunit Governs RNA Polymerase Stability and Transcriptional Specificity in Staphylococcus aureus

“…As the disruption of rpoE results in slower bacterial growth in a variety of organisms (e.g., an extended lag phase [8,51,52]), removal of this subunit from RNAP may actually present a survival advantage during stress, redirecting resources away from division and toward repair and cellular maintenance. In agreement with this is a recent study with Streptococcus pneumoniae biofilms, where there appears to be selective pressure for rpoE mutations leading to small-colony variant (SCV) phenotypes (53). SCV formation is a common mechanism used by many different bacteria which would initially appear to present a defect in viability but in actuality results in enhanced survival (54) and antibiotic resistance and the development of persister cells (55).…”

Puzzling Over the Pneumococcal Pangenome

“…These efforts are focused on protective and widespread protein antigens as well as on the development of whole cells vaccines ( Miyaji et al, 2013 ; Rosch, 2014 ; Moffitt and Malley, 2016 ; Wilson et al, 2017 ). In parallel, experimental evolution in in vitro biofilms provide insights into adaptation in vivo ( Churton et al, 2016 ; Cowley et al, 2018 ). Current studies suggest the revolutionary idea that we may be in a position to predict the genomic composition of dynamic pneumococcal populations and their responses to vaccines and therapies.…”

What drives parallel evolution?

“…Clonal interference, the competition that occurs between beneficial mutations occurring simultaneously on different genetic backgrounds within large populations, can further increase the likelihood that the same, large effect mutations will fix in independent populations. Escherichia coli REL1206 1 [42] Escherichia coli K12MG1655 1 [43] Escherichia coli K12MG1655 1 [44] Escherichia coli K12 deletions 22 [45] Escherichia coli MC100 3 [11] Pseudomonas fluorescens SBW25 5 [39] Pseudomonas aeruginosa PA14 4 [46] Streptococcus pneumoniae Serotype 22F 1 [47] Yersinia pestis Yp1945, Yp2126 2 Fungi [48] Saccharomyces cerevisiae 288c 1 [49] Saccharomyces cerevisiae 288c 2 [50] Saccharomyces cerevisiae 288c 1 [37] Saccharomyces cerevisiae DBY15084 2 [51] Saccharomyces cerevisiae BY4741 1 [52] Saccharomyces cerevisiae BY4741 1 [53] Saccharomyces cerevisiae BY4741 deletions 14…”