The theory and practice of evolvability: Effects and mechanisms of mutation rate plasticity

Spontaneous mutation is a key engine of evolution and is central to organisms' 'evolvability'. Thus understanding mutation is important for understanding the fundamentals of the mechanisms that have generated all the diversity of life we see today. It is also important for combatting undesirable evolution, such as antibiotic resistance in microbes. Others have found that mutation rates can vary between organisms (genotypes) and locally within an organism's genome and that rates can evolve by natural selection. We have found that the chances that a single genotype mutates can also vary, mediated by cell-cell communication. Variation of this type is predicted by mathematical theory to increase organisms' evolvability, allowing them to adapt quicker. However, there are still important gaps in our understanding of this area. Firstly, we do not know whether the system we have identified actually has this predicted effect on evolution. Secondly we do not understand the mechanism - what signal mediates the cell-cell communication used here and how it acts. Finally, while the theory predicted the existence of variable mutation rates of the sort we observe and their beneficial effect on evolvability, it didn't predict the sort of cell-cell communication mechanism we have identified and cannot yet deal with such processes.

In this project we shall address each of these issues, considering the rate of evolution of antibiotic resistance in the gut microbe Escherichia coli. Firstly we shall investigate the mechanism by which cell-cell signals affect mutation rate. We already know that this mechanism requires a particular gene (luxS) whose removal affects multiple signalling molecules. By experimentally manipulating genes and small molecules involved in the biochemical network in which luxS is involved and its downstream effects, we shall understand better how this signalling is achieved. Secondly we shall develop the theory and carry out computational experiments to include the sort of cell-cell communication mechanisms we observe and understand how exactly they may affect the course of evolution. This will also provide new hypotheses that may be tested in the lab. Finally we shall test whether and when this control of mutation rate actually is beneficial to the organism's evolution (as predicted by theory) by watching evolution happen in the laboratory with and without the ability to vary mutation rate in this way.

Together, this work will link the theory and reality of evolvability, using very different scientific disciplines to determine when, how and why organisms vary their mutation rates.

We propose to test the mechanism and role of mutation rate plasticity (that is variation in mutation rate within a single genotype) in the process of evolutionary adaptation. Experiments will primarily be in the bacterium Escherichia coli with complementary computational models to keep a close link with theory, which will also be developed here. Central to this proposal is our recent discovery that, consistent with theory, the rate of mutations conferring rifampicin resistance (RifR) is inversely related to the density of cells (i.e. high mutation rates at low cell densities and vice versa). This relationship depends on the key quorum-sensing gene luxS and is non-cell-autonomous (i.e. mutation rate is socially determined - mutation rate depends on the genotype of co-cultured cells). With our proposed study we shall 1) test hypotheses regarding the details of the signalling system involved; specifically, luxS deletion affects at least two autoinducers, AI-2 and AI-3, we shall discover which, if either is involved. 2) Develop existing theory, based on Fisher's geometric model of adaptive evolution and use numerical simulations to identify the circumstances under which density-dependent mutation rate may be adaptive. 3) Use experimental evolution to test the hypothesis, already available from theory, that this sort of mutation rate plasticity is adaptive under some circumstances, i.e. enables a more rapid rate of evolution (increased 'evolvability').

In this way we will evaluate the contribution of mutation rate plasticity to 'evolvability' and get a direct insight of how quorum-sensing mediated social interactions affect evolutionary trajectories.

Who will benefit from the research?
Beneficiaries will include:
- The wider academic scientific community, especially those with interests in evolution, microbiology, infectious disease, evolutionary computation, and interdisciplinary approaches to biology.
- Commercial companies with interests in anti-microbial or anti-virulence strategies.
- University students, school children and the general public interested in evolution or combatting microbial disease.
- The staff employed on this project.

How will they benefit?

Our findings will be of wide scientific interest well beyond the immediate academic fields of those involved. The development of this E. coli system as a model of density-dependent mutation rate plasticity (particularly through the use of theory and in silico modelling) will enable extrapolation or transfer to many other systems, notably microbial pathogens and potentially to eukaryotic systems as well. The computational modelling and theory will in itself be relevant and useful to those who are interested addressing complex optimisation problems in a wide range of fields (e.g. operations research). Students and the public have a real fascination with evolution plus a, frequently personal, interest in combatting disease and related subjects such as anti-microbial resistance. Therefore this work provides an ideal subject to engage in dialogue about the mechanisms of evolution, reinforcing and feeding these interests, thus promoting an interest in science generally.

What will be done to ensure that they benefit?

We will continue to publish in as high impact journals as possible. We will also present our work at international and national conferences, both specialist and general. This will not only disseminate our work, but also add to the experience of the researchers employed, enhancing their employability and ability to contribute to science in the future. We will approach the commercial R&D sector with the aid of our Faculty Research Business Managers and the University of Manchester Intellectual Property Company (UMIP). Both PI and Co-Is are active in teaching specialist courses and new findings will also be disseminated by this route. The Faculty in Manchester has a full time Schools Liaison Officer with whom we shall identify opportunities for school engagement. Engagement with the general public will include enhancing our web presence (facilitated by our respective Faculty Media Officers).