Competitive Fitness During Feast and Famine: How SOS DNA Polymerases Influence Physiology and Evolution inEscherichia coli

Abstract

Escherichia coli DNA polymerases (Pol) II, IV, and V serve dual roles by facilitating efficient translesion DNA synthesis while simultaneously introducing genetic variation that can promote adaptive evolution. Here we show that these alternative polymerases are induced as cells transition from exponential to long-term stationary-phase growth in the absence of induction of the SOS regulon by external agents that damage DNA. By monitoring the relative fitness of isogenic mutant strains expressing only one alternative polymerase over time, spanning hours to weeks, we establish distinct growth phase-dependent hierarchies of polymerase mutant strain competitiveness. Pol II confers a significant physiological advantage by facilitating efficient replication and creating genetic diversity during periods of rapid growth. Pol IV and Pol V make the largest contributions to evolutionary fitness during long-term stationary phase. Consistent with their roles providing both a physiological and an adaptive advantage during stationary phase, the expression patterns of all three SOS polymerases change during the transition from log phase to long-term stationary phase. Compared to the alternative polymerases, Pol III transcription dominates during mid-exponential phase; however, its abundance decreases to ,20% during long-term stationary phase. Pol IV transcription dominates as cells transition out of exponential phase into stationary phase and a burst of Pol V transcription is observed as cells transition from death phase to long-term stationary phase. These changes in alternative DNA polymerase transcription occur in the absence of SOS induction by exogenous agents and indicate that cell populations require appropriate expression of all three alternative DNA polymerases during exponential, stationary, and long-term stationary phases to attain optimal fitness and undergo adaptive evolution.T HE generation of genetic diversity directly impacts the evolutionary fitness of a population, and the molecular mechanisms influencing the formation of allelic variation often dictate success or failure within complex bacterial communities (Chao and Cox 1983;Bjedov et al. 2003;Saint-Ruf and Matic 2006;Pigliucci 2008;Woods et al. 2011). Given that the majority of mutations are introduced during replication, perturbations in the fidelity of replication can have dramatic consequences on the evolutionary trajectory of a population (Yeiser et al. 2002;Kunkel 2004;Foster 2007;Galhardo et al. 2007). Accordingly, characterization of the mechanisms and of the extent to which DNA polymerases introduce genetic variation is critical to understanding the physiology and evolution of bacteria.Escherichia coli encodes five DNA polymerases (Goodman 2002;Johnson and O'Donnell 2005;Friedberg 2006). Highfidelity DNA polymerase III performs the majority of DNA replication under vegetative conditions, with Pol I contributing principally to maturation of Okazaki fragments (Kornberg and Baker 1992;Friedberg 2006). Three alternative DNA polymerases (Pol II, ...

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