Noise in bistable gene regulation

Bacteria follow a bet-hedging tactic to survive the ever changing environment they are living in. If growth conditions become unfavourable only some cells in a bacterial population choose to differentiate into specialized cells. The advantage is that it leaves other cells capable of inducing other survival strategies, and this could be favourable in case the environmental conditions change again. The fact that some cells choose to differentiate whereas other cells do not, whereas they are all genetically the same and live in the same environment, can be achieved by a so called 'bistable' genetic switch. Central to this switch is a positive feedback loop. Activation of this loop requires that the concentration of the activator reaches a certain threshold level in the cell. In bistable switches it is assumed that the concentration of the activator varies between cells and relies on the stochastic fluctuations (noise) in basal mRNA synthesis. In some cells the concentration of activator reaches the threshold level and in such cells the auto-stimulatory feedback loop is switched on. Thus, noise in basic cellular processes is an essential factor in bistable gene regulation. However, which of the cellular processes contribute most to this noise is debatable. The prevailing view is that differences in transcriptional activities provide the main source of noise in bacteria. However, in this proposal I put forward other basic cellular processes, including growth rate, cellular localization of proteases and DNA replication as possible major factors in the activation of bistable gene regulation. A popular model system to study bistable gene expression is the development of genetic competence in the bacterium Bacillus subtilis. This cellular state enables the bacterium to take up and incorporate extracellular DNA with the potency to gain useful genetic material. At the centre of the competence signal transduction cascade lays the auto-stimulatory activation of the competence transcription factor ComK. This positive feedback loop is responsible for the bistable nature of competence development, and this feedback loop will be used to investigate what the main sources of noise are that determine the outcome of this bistable switch. It is now apparent that bistable differentiation processes are ubiquitous and are also part of essential differentiation pathways in higher eukaryotes. In addition, pathogenic microorganisms use bistable regulation to evade antibiotic treatment. Moreover, the seemingly unpredictable behaviour of individual cells in bacterial populations poses difficulties in the biotech and food industry, as well. Because of the wide spread implications it is essential to gain more knowledge on the basic cellular processes that govern the outcome of bistable switches.

Bacteria follow a bet-hedging tactic to survive the ever changing environment they are living in. In isogenic populations only a subset of cells differentiate into specialized cells, for example spores. This leaves other cells capable of inducing other survival strategies, which could be more favourable in case the environmental conditions change again. Differentiation in a limited number of cells can be achieved by a so called 'bistable' genetic switch that is comprised of an auto-stimulatory feedback loop. According to the prevailing view the ultimate decision to activate this feedback loop is random and depends on the stochastic fluctuations (noise) in mRNA synthesis. In this proposal I put forward that noise in other basic cellular processes, including growth rate, cellular localization of proteases, DNA replication, and/or DNA-binding activities can be major factors in the activation of bistable gene regulation. A popular model system to study bistable gene expression is the development of genetic competence in the bacterium Bacillus subtilis. At the centre of the competence signal transduction cascade lays the auto-stimulatory activation of the key competence transcription factor ComK. This positive feedback loop is responsible for the bistable nature of competence development, and will be used to investigate what the main sources of noise are that determine the outcome of competence. It is now apparent that bistable differentiation processes are ubiquitous and are also part of essential differentiation pathways in higher eukaryotes. There is information that the heterogenic result of positive feedback regulation is used by pathogens to survive antibiotic treatment as persisters. The seemingly unpredictable behaviour of individual cells in bacterial populations causes concerns in the biotech and food industry, as well. Because of the wide spread implications it is essential to gain more knowledge about the cellular processes that govern bistability.

Who will benefit? - The wider public - UK scientific competitiveness - Biotech companies - The postdoc on the project How will they benefit? The wider public: Bacterial pathogens use bistable gene regulation as a means to create a variety of phenotypes within the population. This bet-hedging strategy enables them to become dormant and as such survive antibiotic treatment (persister phenotype). The phenotypic variability of bacterial cultures poses also problems in the food industry, since it complicates the killing of food spoilage bacteria. Infectious diseases are a serious burden on healthcare. The growing number of multi-drug resistant bacteria that emerges requires the development of new treatments. If we want to be able to fight infectious diseases in the long run, it is pivotal to understand the essential functions of pathogens, including basic processes like bistable gene regulation, which is the focus of this proposal. UK scientific competitiveness: Bistable gene regulation has been the subject of several recent high-profile papers, and it is a competitive field of research when it comes to the study of model systems such as competence development in B. subtilis. Research on bistable gene regulation is so far limited in the UK. Successful implementation of this proposal will therefore strengthen the scientific competitiveness of the UK. As a member of the UK StoMP research network (Stochastic Modelling for Prokaryotes) I have had extensive discussions on modelling bistable regulation pathways. The model system in my research proposal is ideally suited for mathematical modelling, and if successful, I will collaborate on this with Dr. Rosalind Allen, of the School of Physics and Astronomy at Edinburgh University (support letter is included). Such collaborations will further add to the scientific competitiveness of the UK. Biotech companies: B. subtilis is a commercial production organisms used in the biotech industry. Also in bioreactors the cell-to-cell variability can be substantial, and this can reduce yields. One such company that uses B. subtilis is DSM Nutritional Products (Headquarter in Basel, and production facilities in Dalry and Belfast). DSM Nutritional Products is a global company that is the world's leading supplier of vitamins, carotenoids and other fine chemicals to the feed, food, pharmaceutical and personal care industries. They showed a great interest in my research on bistable gene regulation and provided a support letter to endorse this proposal. The knowledge emerging from the proposed research could eventually help to increase production yields in B. subtilis. The postdoc on the project: The postdoc has to present the data on international scientific meetings. The presentation skills obtained during the project will be useful in all relevant employment sectors. Moreover, B. subtilis is a model system for Gram-positive bacteria and also used as a production organism in the industry. The wide use of this bacterium will increase employability. What will be done to ensure that they benefit? The wider public: The results of the research will be published in peer reviewed scientific journals that make their publications readily available to the public (open access policy). UK scientific competitiveness: Collaborations with biophysicists such as Dr. Rosalind Allen will be initiated. Biotech companies: When it is foreseen that the results of the research has potential commercial relevance, contact with biotech companies will be established. In addition, I will have regular contact with Dr. Zoltan Pragai from DSM Nutritional Products, to discuss our progress on bistable gene regulation. The postdoc on this project: The postdoc will attend international scientific meetings to present the work.