Post-transcriptional feedback control of polyamine metabolism in yeast: an integrated modelling and experimental investigation

Lead Research Organisation: University of Leicester
Department Name: Engineering

Abstract

The cell is the basic unit of life, and a typical multi-celled organism like a human is made up of literally millions of such building blocks. Within each cell, thousands of chemical reactions take place, controlling everything from energy generation to DNA manufacture. All these chemical reactions are enclosed within the membrane that surrounds the cell. One set of such chemical reactions forms the focus of this research proposal, and is involved in the manufacture of a series of important compounds called polyamines. Polyamines are small molecules that play a crucial role in cell health and viability, and without them, life would be unsupportable. Changes in the levels of polyamines can cause cell death or cancer, as well as human genetic disease like the mental retardation disorder Snyder-Robinson Syndrome. Polyamines help support a range of processes central for viability. For instance, they help DNA to be correctly packaged and folded. In doing so, they help the genes encoded in the DNA to be correctly switched on and off, or 'expressed'. Polyamines also help another polymer called RNA to fold correctly, and again, RNA plays a central role in gene expression. As a final example, polyamines help protect the membrane in the cell from damage by the oxidising chemicals generated accidentally in the cell when energy is generated; as such, polyamines play a very similar role to vitamin C, an important anti-oxidant found in our diet. In a factory or chemical plant, chemical reactions are always carefully controlled, and in this respect, the cell is no different. Its chemical reactions are also subject to a series of checks and balances perfected over the course of evolution to make sure the reactions can be turned on, or off, as more or less product is required. Without this control, living systems would not exhibit the ability to respond to changes in the environment, and indeed, in some cases, would cease to be viable. The requirement for effective, tight control has resulted in many cellular chemical reactions, including those of polyamine synthesis, being subject to complex, multiple and interlocking controls. Understanding how control over polyamine synthesis operates in a living cell, how robust that control is, and under what circumstances the control might break down, for example in a disease state like cancer or Snyder-Robinson Syndrome, is a problem that can only be addressed by the new field of systems biology. In systems biology, biologists work in multi-disciplinary teams with physical scientists such as control engineers to try and understand how biological control processes interact to enable robust control to be exerted. This interdisciplinary approach is required as a direct response to the complexity of the polyamine control mechanisms being studied, which renders standard biological research approaches inadequate. In this proposal, biologists and control engineers will be working together in an interdisciplinary team to subject the polyamine synthesis pathway to a systems biology analysis. Mathematical models of the biochemical reactions will be developed, tested and employed to test hypotheses about how the pathway functions. The aim is to understand how polyamine manufacture is controlled, to understand what goes wrong with the control processes in human disease states, and to understand how robust polyamine control is i.e. how successfully is control maintained despite changes in cell biochemistry. The research project will reveal how control over this key metabolic process is exerted in a healthy cell, and how that control goes wrong in different disease states.

Technical Summary

Polyamines are small poly-cationic molecules found in all eukaryotes and bacteria. They perform an essential role in a number of core cellular processes, including protection of membranes from oxidation, and DNA transcriptional silencing. Their synthesis in the cell is subject to multiple and complex controls, most operating at the post-transcriptional level. Of these, the most important is the polyamine-regulated translation of a protein called antizyme, which in turn regulates the stability of ornithine decarboxylase, the first enzyme in polyamine biosynthesis. Defects in polyamine biosynthesis can give rise to a number of different human pathologies, but because of the system complexity, full understanding of how the control systems respond to these natural perturbations is only possible in the context of a predictive and working model of the pathway and its control. This proposal will generate and validate such a mathematical model of polyamine biosynthesis, and use that model to examine how robust polyamine pathway post-transcriptional control mechanisms are to perturbation, and how the biochemical 'engineering' of different elements of the polyamine control network contribute to the overall system behaviour in health and disease states.

Publications

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Related Projects

Project Reference Relationship Related To Start End Award Value
BB/F019602/1 13/10/2008 12/03/2010 £188,540
BB/F019602/2 Transfer BB/F019602/1 26/05/2010 25/08/2011 £94,337
 
Description In this study, a novel quadruple yeast gene knockout
strategy was devised in which de novo synthesis and metabolic interconversion of supplied polyamines is prevented. Using this tool, this study aimed to define for the first time how each of the polyamines individually stimulates the frameshifting, termination and readthrough events at the antizyme frameshift site in vivo. With this information, a predictive mathematical model of the ribosomal frameshift controller could then be generated which will form the cornerstone of future systems biological analysis of polyamine biosynthesis.
Exploitation Route The model developed in this study not only helps define the workings of a key metabolic pathway important in a number of human pathologies, but will also allow the introduction of novel translational-based feedback control modules to the synthetic biologist's toolkit.
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology