title: Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens.
abstract: Phenotype switching is commonly observed in nature. This prevalence has allowed the elucidation of a number of underlying molecular mechanisms. However, little is known about how phenotypic switches arise and function in their early evolutionary stages. The first opportunity to provide empirical insight was delivered by an experiment in which populations of the bacterium Pseudomonas fluorescens SBW25 evolved, de novo, the ability to switch between two colony phenotypes. Here we unravel the molecular mechanism behind colony switching, revealing how a single nucleotide change in a gene enmeshed in central metabolism (carB) generates such a striking phenotype. We show that colony switching is underpinned by ON/OFF expression of capsules consisting of a colanic acid-like polymer. We use molecular genetics, biochemical analyses, and experimental evolution to establish that capsule switching results from perturbation of the pyrimidine biosynthetic pathway. Of central importance is a bifurcation point at which uracil triphosphate is partitioned towards either nucleotide metabolism or polymer production. This bifurcation marks a cell-fate decision point whereby cells with relatively high pyrimidine levels favour nucleotide metabolism (capsule OFF), while cells with lower pyrimidine levels divert resources towards polymer biosynthesis (capsule ON). This decision point is present and functional in the wild-type strain. Finally, we present a simple mathematical model demonstrating that the molecular components of the decision point are capable of producing switching. Despite its simple mutational cause, the connection between genotype and phenotype is complex and multidimensional, offering a rare glimpse of how noise in regulatory networks can provide opportunity for evolution.
authors.affiliation: New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand; Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland; Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.
authors.forename: Jenna
authors.initials: J
authors.lastname: Gallie
authors.affiliation: New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand; Santa Fe Institute, Santa Fe, New Mexico, United States of America.
authors.forename: Eric
authors.initials: E
authors.lastname: Libby
authors.affiliation: New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand; Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.
authors.forename: Frederic
authors.initials: F
authors.lastname: Bertels
authors.affiliation: New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.
authors.forename: Philippe
authors.initials: P
authors.lastname: Remigi
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.
authors.forename: Christian B
authors.initials: CB
authors.lastname: Jendresen
authors.affiliation: New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.
authors.forename: Gayle C
authors.initials: GC
authors.lastname: Ferguson
authors.affiliation: Laboratoire de Physique Statistique (UMR8550), Ecole Normale Superieure, Paris, France; Institut de Biologie de l'ENS (IBENS UMR 8197), Ecole Normale Superieure, Paris, France; Universite Paris Diderot, Paris, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Desprat
authors.affiliation: Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.
authors.forename: Marieke F
authors.initials: MF
authors.lastname: Buffing
authors.affiliation: Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.
authors.forename: Uwe
authors.initials: U
authors.lastname: Sauer
authors.affiliation: New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand; Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
authors.forename: Hubertus J E
authors.initials: HJ
authors.lastname: Beaumont
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Jan
authors.initials: J
authors.lastname: Martinussen
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Mogens
authors.initials: M
authors.lastname: Kilstrup
authors.affiliation: New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand; Max-Planck Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Paul B
authors.initials: PB
authors.lastname: Rainey
mesh_terms: D016667:Bacterial Capsules / Q000378:metabolism; D005075:Biological Evolution; D015964:Gene Expression Regulation, Bacterial; D005838:Genotype; D053858:Metabolic Networks and Pathways / Q000235:genetics; D015233:Models, Statistical; D010641:Phenotype; D011134:Polysaccharides / Q000096:biosynthesis*; D011135:Polysaccharides, Bacterial / Q000096:biosynthesis*; D011551:Pseudomonas fluorescens / Q000235:genetics* / Q000378:metabolism / Q000648:ultrastructure; D011743:Pyrimidines / Q000096:biosynthesis*
chemical_list: D011134:Polysaccharides; D011135:Polysaccharides, Bacterial; D011743:Pyrimidines; C004275:colanic acid; C030986:pyrimidine