Translational responses to stress: a global view

Our bodies are made of very different types of cells: Skin cells are flat and protect our body, while brain cells have cables that pass messages around. Despite being so different, all our cells carry exactly the same information in their genes. What makes them special is what information they use, that is, which genes they switch on and off.

Cells need to respond to changes in their environment (stress) to avoid damage or even death. Stress conditions include high or low temperatures, lack of nutrients or a poor supply of oxygen. Cells react to stress by varying the way in which they use the information from their genes.

The information on how to make a cell is stored in the form of a DNA molecule. However, this information cannot be read directly: it first needs to be copied into another molecule called messenger RNA (mRNA), from which it can be 'translated' into a protein. Proteins are the components that directly build the cell and make it function, and it is also proteins that are responsible for protecting the cell from the damage caused by stress.

Cells react to stress by switching on 'defence' genes and by switching off the genes that are not needed during the response to stress. The process of turning on and off genes often takes place at the level of the translation of messenger RNAs (that is, by selecting which messenger RNAs will be translated into proteins). Studying translation is relevant for human cells, because the mechanisms that regulate translation often go awry during cancer and several inherited conditions.

Our aim is to understand how cells change the information they use - especially through translation - to cope with situations of stress. A recently-developed experimental technique allows the simultaneous detection of the translation of every messenger RNA in the cell, thus providing unprecedented insight into how cells regulate translation. The method is called 'ribosome-profiling' after the ribosome, which is the cellular machine that carries out translation. We will apply this approach to study how cells modify translation of messenger RNAs in response to several stress conditions.

One way to study a complicated process of the human body is to use a model organism: this is a simpler creature, but similar enough to allow us to learn about ourselves. To study these questions we will employ a simple yeast -made of a single cell- that can react to many different types of stress. We will investigate how the yeast cells regulate translation in response to stress: which mechanisms they use, which genes are turned on an off, and what is the importance of these genes.

We expect this information will be useful to understand how human cells behave and, eventually, help us devise cures for disease.

Cells react to stress conditions by reprogramming translation. This response involves a general down-regulation of translation coupled to increased translation of specific transcripts. A novel approach, called ribosome profiling, has revolutionized the study of translation programs. This method allows the genome-wide estimation of translation rates and the systematic identification of translated regions. Although this approach has been applied to specific stresses and experimental systems, it has not been performed systematically for multiple stresses under comparable conditions.

We will use the fission yeast Schizosaccharomyces pombe to study how cells remodel translation under stress situations. We will apply ribosome profiling (to measure translation) and RNA-seq (to estimate RNA levels) to S. pombe cells subject to five different stress conditions. This will be done for wild type cells and for mutants with impaired key response pathways. These experiments will provide information on the nature of the genes regulated upon stress, and on the coordination of translational and transcriptional programs. Moreover, the data will shed light on the mechanisms that repress global translation, and on how specific mRNAs become resistant to general down-regulation. Finally, we will use published information and our datasets to generate testable hypotheses that will be followed up using genetic and biochemical approaches. For example, to investigate if resistance to inhibition is achieved through the use of specialised components of the general translation machinery, we will examine translation in mutants in a specific isoform of the eIF4E translation factor that is required for resistance to specific stresses.

These studies will provide an overview of the nature, extent and molecular mechanisms of translational reprogramming in response to stress. We expect that this work will allow the discovery of general principles that may be applicable to human cells.

This project will contribute to the training of researchers in key areas of research, and will result in knowledge that may have long-term implications in various areas of medical research as described below.

The biotechnology and pharmaceutical industries are potential beneficiaries of this project, both through the training of highly qualified researchers (point 1) and the knowledge and expertise it will generate (points 2 and 3). In addition, the project may contribute to fighting human disease, which would benefit the general public (points 2 and 3). The 'Pathways to Impact' document discusses in detail how we will ensure that the potential beneficiaries of this project will be reached.

1] Training and capacity building in functional genomics / systems biology. This project will provide an excellent opportunity for the training of the postdoctoral researcher in state-of-the-art genomic methods and in the analysis of large scale genomic datasets (which will require the acquisition of programming skills). This will be done through the work carried out in the laboratory, as well as through courses and interactions with members of the Cambridge Systems Biology Centre. The provision of scientists trained in these multidisciplinary approaches will be beneficial for the UK industry, especially the biotechnology and pharmaceutical sectors. Indeed, a former postdoc who recently left my laboratory is now working for a UK Biotechnology company. This is a key objective of the BBSRC Strategic Plan Enabling Theme 1 'Enabling innovation', which states that 'as bioscience becomes increasingly quantitative, there is also an urgent need to raise the mathematical and computational skills of biologists at all levels', and defines as a key priority 'training of bioscience researchers, particularly around our three strategic priorities and in the development of mathematical and computational skills'. Training in new technologies is also a key priority of Enabling Theme 2 'Exploiting new ways of working', which aims to 'enhance skills and capacity to exploit new tools and approaches e.g. through training for researchers'.

2] General understanding of human disease: Defects in the regulation of translation have been implicated in several human diseases including cancer. For example, many initiation factors are overexpressed in cancer tissues, and their increased expression correlates with malignancy and poor prognosis (1). Moreover, numerous inherited syndromes are due to mutations in genes encoding translation factors or regulators of translation, as well as to mutations that alter RNA regulatory sequences (such as uORFs or binding sites of RNA-binding proteins) (2). This proposal aims at identifying general principles of how translation is regulated, which may be applicable to human cells.

3] As described in more detail in the 'Academic Beneficiaries' section, recent work has shown similarities between pathogens of the Pneumocystis genus and fission yeast (in particular, in their meiotic pathways). These organisms cause pneumonia in patients with weakened immune systems (premature babies, AIDS and cancer patients). As Pneumocystis cannot be cultured in vitro, there is a need for model systems that allow the study of their basic biology. As stress responses are essential for the survival of microorganisms, our results might be useful to understand the biology of these pathogens and develop treatments against their infection. To make sure this information reaches the Pneumocystis research community, we will highlight these similarities in peer-reviewed publications, our website and relevant scientific conferences.

(1) Ruggiero 2013 'Translational control in cancer etiology', Cold Spring Harb Perspect Biol. 1;5(2)
(2) Scheper et al. 2007 'Translation matters: protein synthesis defects in inherited disease', Nature Reviews Genetics 8, 711-723