Characterisation of a novel bacterial ribonucleoprotein complex analogous to eukaryotic processing (P) bodies in Escherichia coli

Bacteria need nutrients to grow. However, in the environment or in the human body, bacterial growth is often compromised by nutrient limitation. Hence, bacteria spend the majority of their time in a starved and thus non-growing state. The processes that allow bacteria to cope with nutrient starvation begin with the synthesis of RNA - the first step in the reaction that switches on genes. Therefore, it is important to understand how the RNA, once synthesized, is managed to allow bacterial cope with nutrient starvation. This will allow us design novel interventional strategies to combat disease causing bacteria. In this project, since nitrogen represents an essential element of most molecules in the bacterial cell, we will use nitrogen starvation as a model nutrient stress to study in detail, how the bacterium Escherichia coli manages RNA. In particular, we will study in detail a novel 'site of RNA storage' in the E. coli, which we discovered to play an important role in how E. coli copes with nitrogen starvation. We posit that this 'site of RNA storage' could be akin to a similar feature, called the P-body, which is often formed in stressed cells found in our bodies and that of other animals. In summary, the results of this project will advance our fundamental knowledge of how the bacterial cell functions and thereby provide us with the much-needed new information and inspiration to control disease causing bacteria.

Bacteria in their natural environments seldom encounter conditions that support continuous growth. Hence, many bacteria spend the majority of their time in states of little or no growth because they are starved of essential nutrients, including carbon, nitrogen and transitional metals. To cope with prolonged periods of nutrient starvation, bacteria have evolved complex adaptive strategies, which enable them to survive until conditions become favourable for growth. Bacteria respond to nutrient deficiency by remodelling their transcriptome through regulating of RNA primarily at the level of synthesis, metabolism and degradation. Although our knowledge of the mechanisms that underpin RNA regulation in bacteria growing under nutrient replete conditions is substantially advanced, our understanding of RNA regulation in nutrient starved and thus growth-attenuated bacteria is still in its infancy. This represents an important gap in our understanding of basic and applied bacterial physiology. Ribonucleoprotein complexes called processing (P) bodies are widespread in eukaryotic cells and represent important structures for RNA regulation. We now present hitherto unreported evidence for the formation of P body-like complexes in the subcellular landscape of nutrient starved and growth attenuated Escherichia coli experiencing long-term nitrogen starvation. The aim of this project is to characterise the properties and composition of these novel bacterial nutrient stress response associated ribonucleoprotein complexes, to reveal whether they are bacterial analogues of eukaryotic P bodies and establish their role in shaping the RNA landscape in long-term nitrogen starved E. coli. Collectively, a better knowledge of the processes of RNA regulation in nutrient starved and growth attenuated bacteria would not only facilitate its exploitation for developing new antibacterial targets, but also contribute broadly to our understanding of bacterial cell function and stress response.

This project clearly falls within the key remit of the BBSRC to support world-class fundamental bioscience research that underpins and impacts human health and addresses the major responsive mode priorities 'combatting antibiotic resistance'. The following impact milestones, which are described in detail with timelines in the pathways to impact document, have been identified:

1. To advance fundamental understanding of bacterial cell function, especially, how bacteria cope with nutrition stress (via primary publication, conference attendance and collaborations).
2. To explain to lay audiences about how bacteria cope with nutrient stress and why this fundamental knowledge and understanding is important for tackling global challenges such as bacterial resistance to antibiotics. To ensure timely communication of research output to lay audiences via local press portals.
3. To collaborate, as required, with industrial partners to maximise the translational potential of funded research.
4. To train the next generation of UK bioscientists and enable the development of international research networks to benefit and disseminate UK knowledge economy and capability abroad.