Academic journal article Genetics

Metabolic Changes Associated with Adaptive Diversification in Escherichia Coli

Academic journal article Genetics

Metabolic Changes Associated with Adaptive Diversification in Escherichia Coli

Article excerpt

ABSTRACT

During a 1000-generation evolution experiment, two types of morphologically and kinetically distinct bacteria repeatedly diverged from a common ancestor in a fully sympatric seasonal environment containing glucose and acetate. To investigate the metabolic modifications associated with this adaptive diversification, we compared transcription profiles of the two derived types and the common ancestor. Both derived types share a suite ofcommonmetabolic changes that may represent adaptation to the environment preceding the diversification event. These include improved translation efficiency, glucose uptake capacity via the mal/lamB genes, upregulation of various transporters during stationary phase, and likely the disruption of the rbs operon. The diversification event is associated with the overexpression of genes involved in the TCA cycle, glyoxylate shunt, acetate consumption, and anaerobic respiration in one type and in acetate excretion in the other. These results reveal that competition for both carbon and oxygen have likely played an important role in the adaptation of Escherichia coli during this adaptive diversification event, where one derived type mainly consumes glucose at a fast rate when oxygen is not limiting, and the other derived type consumes glucose and acetate at a slower rate, even when oxygen is limiting.

LINKING genetic, biochemical, and physiological changes to evolutionary processes is difficult. One of the most important reasons for this is due to the nature of descent with modification: evolutionary processes occur over long periods of time. One must thus often infer history and ancestry from the standing biological diversity without the actual knowledge of the ancestral states that would allow tracking biological changes. For the last few decades, experiments with quickly reproducing organisms, such as bacteria, evolving under controlled conditions in the lab for hundreds or thousands of generations, have been a powerful alternative to classic comparative studies for better understanding of various evolutionary processes (see Elena and Lenski 2003 and Kassen and Rainey 2004 for reviews). Another difficulty when linking cellular and evolutionary processes is the lack of precise genetic, biochemical, and physiological knowledge in most of the biological systems used as models in evolution studies. Classic genetic and physiological microbial models, such as yeast and bacteria, offer a powerful alternative. By coupling evolution experiments and genetic investigations in these microorganisms, several studies have identified cellular functions involved in evolutionary processes (e.g., Treves et al. 1998; Notley-Mc R obb and Ferenci 1999; Cooper et al. 2001; Spencer et al. 2007). However, in most of the cases, these studies focus on specific candidate genes, and general investigations of metabolic changes are rare (but see Kurlandzka et al. 1991; Cooper et al. 2003; Pelosi et al. 2006). Moreover, most such studies concentrate on understanding directional adaptation to optimize performance in a given environment.

We investigate the evolutionary changes in metabolic functions that occur when a population diversifies. Diversification that leads to the coexistence of several types of bacteria from a single ancestral strain is a frequent outcome of evolution experiments (see, for example, Rosenzweig et al. 1994; Rainey and Travisano 1998; Rozen and Lenski 2000; Friesen et al. 2004). In fact, many of the reported diversification events are consistent with the process of adaptive diversification (Dieckmann et al. 2004) that occurs under sympatric (well-mixed) conditions due to competition for limiting resources. In this study, we take advantage of the short generation time and extensive genetic knowledge of the bacterium Escherichia coli to investigate metabolic changes that occurred during such an adaptive diversification event. According to theory, populations undergoing adaptive diversification experience two different evolutionary phases. …

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