Goldstein RA, Soyer OS. Evolution of taxis responses in virtual bacteria: non-adaptive dynamics.
PLoS Comput Biol 2008;
4:e1000084. [PMID:
18483577 PMCID:
PMC2386285 DOI:
10.1371/journal.pcbi.1000084]
[Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Accepted: 04/07/2008] [Indexed: 11/17/2022] Open
Abstract
Bacteria are able to sense and respond to a variety of external stimuli, with responses that vary from stimuli to stimuli and from species to species. The best-understood is chemotaxis in the model organism Escherichia coli, where the dynamics and the structure of the underlying pathway are well characterised. It is not clear, however, how well this detailed knowledge applies to mechanisms mediating responses to other stimuli or to pathways in other species. Furthermore, there is increasing experimental evidence that bacteria integrate responses from different stimuli to generate a coherent taxis response. We currently lack a full understanding of the different pathway structures and dynamics and how this integration is achieved. In order to explore different pathway structures and dynamics that can underlie taxis responses in bacteria, we perform a computational simulation of the evolution of taxis. This approach starts with a population of virtual bacteria that move in a virtual environment based on the dynamics of the simple biochemical pathways they harbour. As mutations lead to changes in pathway structure and dynamics, bacteria better able to localise with favourable conditions gain a selective advantage. We find that a certain dynamics evolves consistently under different model assumptions and environments. These dynamics, which we call non-adaptive dynamics, directly couple tumbling probability of the cell to increasing stimuli. Dynamics that are adaptive under a wide range of conditions, as seen in the chemotaxis pathway of E. coli, do not evolve in these evolutionary simulations. However, we find that stimulus scarcity and fluctuations during evolution results in complex pathway dynamics that result both in adaptive and non-adaptive dynamics depending on basal stimuli levels. Further analyses of evolved pathway structures show that effective taxis dynamics can be mediated with as few as two components. The non-adaptive dynamics mediating taxis responses provide an explanation for experimental observations made in mutant strains of E. coli and in wild-type Rhodobacter sphaeroides that could not be explained with standard models. We speculate that such dynamics exist in other bacteria as well and play a role linking the metabolic state of the cell and the taxis response. The simplicity of mechanisms mediating such dynamics makes them a candidate precursor of more complex taxis responses involving adaptation. This study suggests a strong link between stimulus conditions during evolution and evolved pathway dynamics. When evolution was simulated under conditions of scarce and fluctuating stimulus conditions, the evolved pathway contained features of both adaptive and non-adaptive dynamics, suggesting that these two types of dynamics can have different advantages under distinct environmental circumstances.
Here, we study how signalling networks mediating chemotaxis could have evolved. We simulated the evolution of virtual bacteria, which can explore their environment by alternating between swimming and tumbling. The tumbling frequency is dictated by the output of a signalling network that senses extracellular nutrient levels, while the bacteria's reproductive success is determined by their ability to find nutrients. Under conditions of abundant food, we find that bacteria quickly evolve signalling networks that enable effective chemotaxis, where increasing nutrient levels increase tumbling frequency. Our findings provide explanation for network dynamics underlying similar behaviour as observed in certain mutant strains of Escherichia coli and in other bacterial species. Conversely, wild-type E. coli respond to increasing nutrient levels by decreasing their tumbling frequency and adapting to constant attractant levels. We observe such adaptive network dynamics when we repeat evolutionary simulations under conditions of scarce food. These findings suggest that (i) adaptation is not necessary for effective chemotaxis, (ii) an ancestral minimal chemotaxis system could have used a simple coupling between the signalling network and the metabolic state, and (iii) environmental conditions are one of the determining factors for the evolution of adaptive responses.
Collapse