Repeated phenotypic evolution by different genetic routes: the evolution of colony switching in Pseudomonas fluorescens SBW25

Abstract

Repeated evolution of functionally similar phenotypes is observed throughout the tree of life. The extent to which the underlying genetics are conserved remains an area of considerable interest. Previously, we reported the evolution of colony switching in two independent lineages of Pseudomonas fluorescens SBW25 (Beaumont et al., 2009). The phenotypic and genotypic bases of colony switching in the first lineage (Line 1) have been described elsewhere (Beaumont et al., 2009; Gallie et al., 2015). Here, we deconstruct the evolution of colony switching in the second lineage (Line 6). We show that, as for Line 1, Line 6 colony switching results from an increase in the expression of a colanic acid-like polymer (CAP). At the genetic level, nine mutations occur in Line 6. Only one of these - a non-synonymous point mutation in the housekeeping sigma factor rpoD - is required for colony switching. In contrast, the genetic basis of colony switching in Line 1 is a mutation in the metabolic gene carB (Beaumont et al., 2009). A molecular model has recently been proposed whereby the carB mutation increases capsulation by redressing the intracellular balance of positive (ribosomes) and negative (RsmAE/CsrA) regulators of a positive feedback loop in capsule expression (Remigi et al., 2018). We show that Line 6 colony switching is consistent with this model; the rpoD mutation generates an increase in ribosome expression, and ultimately an increase in CAP expression.